Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbz Working: n-1-17.cluster.ucsf.bkslab.org:/scratch/xiaobo/236261/xbz-8058088.52 Result: /scratch/xiaobo/236261/xbz-8058088.52 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbz 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/xbz mkdir: created directory `/scratch/xiaobo/236261' mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52' /scratch/xiaobo/236261/xbz-8058088.52 /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/236261/xbz-8058088.52/working' mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/protonate' Storing results in /scratch/xiaobo/236261/xbz-8058088.52/finished Working in /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 /scratch/xiaobo/236261/xbz-8058088.52/working/protonate /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Using inputs as protomers/tautomers. No processing done 461 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/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Bulk generating 3D conformations all protomers in /scratch/xiaobo/236261/xbz-8058088.52/working/3D mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/236261/xbz-8058088.52/working/protonate/xbz-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 ZINC001184488540 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building' mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001184488540 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/1 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184488540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184488540 none CCOC(=O)C[C@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 13, 4, 13, 2, 2, 2, 2, 2, 2, 2, 6, 2, 2, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 24, 24, 24, 24, 24, 4, 4, 2, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488540 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/finished' Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540/0.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488540 Building ZINC001184488541 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488541 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/2 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184488541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184488541 none CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 13, 4, 13, 2, 2, 2, 2, 2, 2, 2, 6, 2, 2, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 23, 23, 23, 23, 23, 4, 4, 2, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/3 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184488541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184488541 none CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 11, 5, 11, 3, 3, 3, 3, 3, 3, 3, 6, 3, 3, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 4, 4, 16, 16, 16, 16, 16, 5, 5, 3, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 7, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488541 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 Building ZINC001184488541 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488541 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 2) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184488541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184488541 none CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 13, 4, 13, 2, 2, 2, 2, 2, 2, 2, 6, 2, 2, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 23, 23, 23, 23, 23, 4, 4, 2, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 3) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184488541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184488541 none CCOC(=O)C[C@@H]1c2cc(OC)c(OC)cc2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 11, 5, 11, 3, 3, 3, 3, 3, 3, 3, 6, 3, 3, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 4, 4, 16, 16, 16, 16, 16, 5, 5, 3, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 7, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488541 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488541 Building ZINC001184488573 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488573 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/4 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488573 none O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 12, 12, 15, 24, 27, 27, 27, 27, 27, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/5 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488573 none O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 14, 24, 27, 27, 27, 27, 27, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488573 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 Building ZINC001184488573 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488573 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 4) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488573 none O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 12, 12, 15, 24, 27, 27, 27, 27, 27, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 5) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488573 none O=C(Nc1cccc(C(=O)N2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 14, 24, 27, 27, 27, 27, 27, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488573 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488573 Building ZINC001184488745 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488745 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/6 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184488745 none CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 10, 19, 19, 10, 10, 5, 10, 10, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 10, 5, 10, 10, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/7 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184488745 none CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 10, 18, 18, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488745 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 Building ZINC001184488745 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488745 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 6) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184488745 none CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 10, 19, 19, 10, 10, 5, 10, 10, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 10, 5, 10, 10, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 7) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184488745 none CN(C)S(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 10, 18, 18, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488745 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488745 Building ZINC001184488628 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488628 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/8 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488628 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 6, 6, 10, 10, 10, 6, 6, 6, 4, 4, 4, 4, 23, 23, 23, 23, 4, 4, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/9 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488628 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 5, 5, 6, 6, 6, 5, 5, 5, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488628 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 Building ZINC001184488628 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488628 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 8) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488628 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 6, 6, 10, 10, 10, 6, 6, 6, 4, 4, 4, 4, 23, 23, 23, 23, 4, 4, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 9) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488628 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 5, 5, 6, 6, 6, 5, 5, 5, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488628 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488628 Building ZINC001184488731 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488731 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/10 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488731 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 5, 5, 6, 6, 6, 5, 5, 5, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/11 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488731 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 5, 5, 9, 9, 9, 5, 5, 5, 4, 4, 4, 4, 23, 23, 23, 23, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488731 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 Building ZINC001184488731 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488731 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 10) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488731 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 5, 5, 6, 6, 6, 5, 5, 5, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 11) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1) `ZINC001184488731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184488731 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H](c4ncn5c4cccc5Br)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 5, 5, 9, 9, 9, 5, 5, 5, 4, 4, 4, 4, 23, 23, 23, 23, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488731 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488731 Building ZINC001184489004 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489004 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/12 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1) `ZINC001184489004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489004 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 11, 11, 11, 8, 8, 8, 4, 18, 18, 18, 18, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/13 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1) `ZINC001184489004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489004 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 12, 12, 12, 8, 8, 8, 4, 19, 19, 19, 19, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489004 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 Building ZINC001184489004 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489004 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 12) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1) `ZINC001184489004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489004 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 11, 11, 11, 8, 8, 8, 4, 18, 18, 18, 18, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 13) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1) `ZINC001184489004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489004 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(I)c4nccn4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 12, 12, 12, 8, 8, 8, 4, 19, 19, 19, 19, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489004 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489004 Building ZINC001184488606 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488606 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/14 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/15 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/16 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/16' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/17 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/17' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488606 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 Building ZINC001184488606 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488606 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 14) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 15) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 16) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 17) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488606 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 Building ZINC001184488606 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488606 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 14) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 15) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 16) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 17) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488606 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 Building ZINC001184488606 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488606 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 14) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 15) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 23, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 7, 7, 7, 5, 5, 5, 10, 10, 10, 23, 23, 23, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 16) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 17) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1) `ZINC001184488606.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488606 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4cc(OC)c(OC)cc4C(=O)C34CCN(C)CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 21, 10, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 8, 8, 8, 5, 5, 5, 10, 10, 10, 21, 21, 21, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488606 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488606 Building ZINC001184488815 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488815 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/18 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21) `ZINC001184488815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184488815 none CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 10, 10, 10, 19, 19, 28, 28, 28, 28, 10, 10, 10, 5, 5, 5, 3, 3, 3, 3, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/19 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21) `ZINC001184488815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184488815 none CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 12, 12, 12, 12, 12, 21, 21, 29, 29, 29, 29, 12, 12, 12, 6, 6, 6, 4, 4, 4, 4, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488815 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 Building ZINC001184488815 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488815 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 18) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21) `ZINC001184488815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184488815 none CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 10, 10, 10, 19, 19, 28, 28, 28, 28, 10, 10, 10, 5, 5, 5, 3, 3, 3, 3, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 19) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21) `ZINC001184488815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184488815 none CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H]1[C@H]2CN(C(=O)OC(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 12, 12, 12, 12, 12, 21, 21, 29, 29, 29, 29, 12, 12, 12, 6, 6, 6, 4, 4, 4, 4, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184488815 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184488815 Building ZINC001184489020 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489020 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/20 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489020 none COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 28, 28, 27, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 27, 27, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 7, 7, 28, 28] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/21 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489020 none COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 26, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5, 34, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489020 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 Building ZINC001184489020 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489020 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 20) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489020 none COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 28, 28, 27, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 27, 27, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 7, 7, 28, 28] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 21) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489020 none COc1ccc(CN2CC[C@@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 26, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5, 34, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489020 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489020 Building ZINC001184489021 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489021 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/22 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489021 none COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 28, 28, 33, 33, 28, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 4, 4, 4, 3, 5, 5, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/23 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489021 none COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 24, 33, 33, 24, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 3, 6, 6, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489021 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 Building ZINC001184489021 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489021 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 22) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489021 none COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 28, 28, 33, 33, 28, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 4, 4, 4, 3, 5, 5, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 23) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489021 none COc1ccc(CN2CC[C@]3(CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 24, 33, 33, 24, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 3, 6, 6, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489021 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489021 Building ZINC001184489180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/24 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(I)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184489180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184489180 none COC(=O)c1sc(I)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'I', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 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: [22, 22, 8, 22, 8, 8, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 8, 8, 22, 22, 22, 8, 5, 8, 8, 8, 11, 11, 11, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/25 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184489180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184489180 none COC(=O)c1sc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'I', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 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: [22, 22, 8, 22, 8, 8, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 8, 8, 22, 22, 22, 8, 5, 8, 8, 8, 11, 11, 11, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 Building ZINC001184489180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 24) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1sc(I)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184489180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184489180 none COC(=O)c1sc(I)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'I', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 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: [22, 22, 8, 22, 8, 8, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 8, 8, 22, 22, 22, 8, 5, 8, 8, 8, 11, 11, 11, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 25) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1sc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184489180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184489180 none COC(=O)c1sc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'I', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 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: [22, 22, 8, 22, 8, 8, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 8, 8, 22, 22, 22, 8, 5, 8, 8, 8, 11, 11, 11, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489180 Building ZINC001184489311 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489311 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/26 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489311 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 23, 32, 23, 23, 23, 23, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 23, 23, 23, 36, 36, 36, 36, 36, 23, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/27 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489311 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 34, 24, 34, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 6, 24, 24, 24, 36, 36, 36, 36, 36, 24, 6, 6, 6, 6, 6, 6, 4, 4, 4, 5, 5, 5, 4, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489311 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 Building ZINC001184489311 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489311 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 26) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489311 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 23, 32, 23, 23, 23, 23, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 23, 23, 23, 36, 36, 36, 36, 36, 23, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 27) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489311 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 34, 24, 34, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 6, 24, 24, 24, 36, 36, 36, 36, 36, 24, 6, 6, 6, 6, 6, 6, 4, 4, 4, 5, 5, 5, 4, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489311 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489311 Building ZINC001184489312 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489312 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/28 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489312 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 21, 34, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 21, 21, 21, 37, 37, 37, 37, 37, 21, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/29 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489312 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 22, 33, 22, 22, 22, 22, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 22, 22, 22, 37, 37, 37, 37, 37, 22, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489312 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 Building ZINC001184489312 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489312 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 28) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489312 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 21, 34, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 21, 21, 21, 37, 37, 37, 37, 37, 21, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 29) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1) `ZINC001184489312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489312 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 22, 33, 22, 22, 22, 22, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 5, 22, 22, 22, 37, 37, 37, 37, 37, 22, 5, 5, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489312 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489312 Building ZINC001184489321 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489321 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/30 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1) `ZINC001184489321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 9, 19, 38, 38, 41, 41, 38, 40, 41, 41, 4, 4, 2, 2, 3, 3, 3, 2, 2, 2, 4, 4, 4, 4, 7, 7, 9, 9, 19, 19, 41, 41, 41, 41, 4, 4, 4, 4, 2] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/31 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1) `ZINC001184489321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 7, 9, 16, 36, 36, 39, 39, 36, 39, 39, 39, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 7, 7, 9, 9, 16, 16, 39, 39, 39, 39, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489321 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 Building ZINC001184489321 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489321 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 30) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1) `ZINC001184489321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 9, 19, 38, 38, 41, 41, 38, 40, 41, 41, 4, 4, 2, 2, 3, 3, 3, 2, 2, 2, 4, 4, 4, 4, 7, 7, 9, 9, 19, 19, 41, 41, 41, 41, 4, 4, 4, 4, 2] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 31) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1) `ZINC001184489321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCN(CCCC(=O)c4ccc(F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 7, 9, 16, 36, 36, 39, 39, 36, 39, 39, 39, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 7, 7, 9, 9, 16, 16, 39, 39, 39, 39, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489321 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489321 Building ZINC001184489332 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489332 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/32 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184489332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489332 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 20, 23, 27, 6, 20, 20, 6, 6, 6, 6, 6, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 6, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 6, 6, 9, 9, 9, 3, 4, 4, 4, 5, 5, 5, 4, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/33 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184489332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489332 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 21, 23, 25, 6, 21, 21, 6, 3, 6, 6, 6, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 6, 27, 27, 27, 27, 27, 25, 25, 25, 25, 25, 6, 6, 8, 8, 8, 3, 4, 4, 4, 5, 5, 5, 4, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489332 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 Building ZINC001184489332 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489332 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 32) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184489332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489332 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 20, 23, 27, 6, 20, 20, 6, 6, 6, 6, 6, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 6, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 6, 6, 9, 9, 9, 3, 4, 4, 4, 5, 5, 5, 4, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 33) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184489332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489332 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 21, 23, 25, 6, 21, 21, 6, 3, 6, 6, 6, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 6, 27, 27, 27, 27, 27, 25, 25, 25, 25, 25, 6, 6, 8, 8, 8, 3, 4, 4, 4, 5, 5, 5, 4, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489332 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489332 Building ZINC001184489394 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489394 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/34 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1) `ZINC001184489394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489394 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 14, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 26, 26, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/35 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1) `ZINC001184489394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489394 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 14, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 26, 26, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489394 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 Building ZINC001184489394 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489394 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 34) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1) `ZINC001184489394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489394 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 14, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 26, 26, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 35) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1) `ZINC001184489394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489394 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(Br)nc3OCC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 14, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 26, 26, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489394 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489394 Building ZINC001184489400 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489400 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/36 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C) `ZINC001184489400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489400 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 11, 11, 11, 26, 28, 28, 32, 32, 32, 32, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 11, 26, 26, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/37 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C) `ZINC001184489400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489400 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 22, 22, 22, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 4, 4, 4, 4, 10, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489400 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 Building ZINC001184489400 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489400 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 36) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C) `ZINC001184489400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489400 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 11, 11, 11, 26, 28, 28, 32, 32, 32, 32, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 11, 26, 26, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 37) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C) `ZINC001184489400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184489400 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)NCC(=O)OC(C)(C)C 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 22, 22, 22, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 4, 4, 4, 4, 10, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489400 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489400 Building ZINC001184489469 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489469 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/38 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 4, 4, 5, 5, 5, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 21, 28, 28, 28, 28, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/39 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 18, 30, 30, 30, 30, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489469 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 Building ZINC001184489469 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489469 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 38) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 4, 4, 5, 5, 5, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 21, 28, 28, 28, 28, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 39) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 18, 30, 30, 30, 30, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489469 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489469 Building ZINC001184489470 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489470 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/40 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489470 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 13, 28, 28, 28, 28, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/41 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489470 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 18, 28, 28, 28, 28, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489470 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 Building ZINC001184489470 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489470 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 40) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489470 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 13, 28, 28, 28, 28, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 41) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1) `ZINC001184489470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489470 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(CC[C@H](C(=O)Nc5cccnc5)O4)[C@@H](C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 18, 28, 28, 28, 28, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489470 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489470 Building ZINC001184489476 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489476 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/42 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489476 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 8, 10, 21, 21, 21, 21, 21, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 21, 21, 21, 21, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/43 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489476 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 11, 21, 21, 21, 21, 21, 2, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 11, 11, 21, 21, 21, 21, 2, 2, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489476 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 Building ZINC001184489476 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489476 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 42) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489476 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 8, 10, 21, 21, 21, 21, 21, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 21, 21, 21, 21, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 43) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489476 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 11, 21, 21, 21, 21, 21, 2, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 11, 11, 21, 21, 21, 21, 2, 2, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489476 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489476 Building ZINC001184489477 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489477 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/44 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489477 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 8, 14, 28, 28, 28, 28, 28, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 14, 14, 28, 28, 28, 28, 2, 2, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/45 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489477 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 11, 26, 26, 26, 26, 26, 3, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 11, 11, 26, 26, 26, 26, 3, 3, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489477 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 Building ZINC001184489477 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489477 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 44) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489477 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 8, 14, 28, 28, 28, 28, 28, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 14, 14, 28, 28, 28, 28, 2, 2, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 45) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489477 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 11, 26, 26, 26, 26, 26, 3, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 11, 11, 26, 26, 26, 26, 3, 3, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489477 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489477 Building ZINC001184489478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/46 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489478 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15, 27, 42, 42, 42, 42, 42, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 27, 27, 42, 42, 42, 42, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/47 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489478 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 22, 37, 37, 37, 37, 37, 3, 5, 5, 6, 6, 6, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 22, 22, 37, 37, 37, 37, 3, 3, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 Building ZINC001184489478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 46) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489478 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15, 27, 42, 42, 42, 42, 42, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 27, 27, 42, 42, 42, 42, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 47) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489478 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4OCCC[C@@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 22, 37, 37, 37, 37, 37, 3, 5, 5, 6, 6, 6, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 22, 22, 37, 37, 37, 37, 3, 3, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489478 Building ZINC001184489479 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489479 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/48 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489479 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 20, 38, 38, 38, 38, 38, 3, 5, 5, 6, 6, 6, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 20, 20, 38, 38, 38, 38, 3, 3, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/49 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489479 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15, 27, 42, 42, 42, 42, 42, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 27, 27, 42, 42, 42, 42, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489479 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 Building ZINC001184489479 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489479 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 48) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489479 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 20, 38, 38, 38, 38, 38, 3, 5, 5, 6, 6, 6, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 20, 20, 38, 38, 38, 38, 3, 3, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 49) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1) `ZINC001184489479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489479 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCCC[C@]4(COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15, 27, 42, 42, 42, 42, 42, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 27, 27, 42, 42, 42, 42, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489479 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489479 Building ZINC001184489496 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489496 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/50 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1) `ZINC001184489496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489496 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 40, 40, 40, 40, 12, 12, 12, 3, 3, 4, 4, 4, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 19, 40, 40, 40, 12, 12, 12, 12, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/51 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1) `ZINC001184489496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489496 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 36, 36, 36, 36, 11, 11, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 17, 36, 36, 36, 11, 11, 11, 11, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489496 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 Building ZINC001184489496 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489496 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 50) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1) `ZINC001184489496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489496 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 40, 40, 40, 40, 12, 12, 12, 3, 3, 4, 4, 4, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 19, 40, 40, 40, 12, 12, 12, 12, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 51) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1) `ZINC001184489496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489496 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)C[C@@H](NC(=O)c3ccsc3)CCO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 36, 36, 36, 36, 11, 11, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 17, 36, 36, 36, 11, 11, 11, 11, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489496 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489496 Building ZINC001184489556 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489556 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/52 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/53 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/54 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/54' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/55 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/55' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489556 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 Building ZINC001184489556 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489556 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 52) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 53) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 54) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 55) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489556 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 Building ZINC001184489556 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489556 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 52) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 53) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 54) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 55) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489556 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 Building ZINC001184489556 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489556 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 52) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 53) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 54) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 8, 8, 8, 8, 16, 22, 22, 22, 22, 22, 8, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 8, 18, 18, 18, 17, 17, 8, 8, 8, 8, 16, 16, 22, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 5, 5, 5, 4, 8, 8, 8, 8] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 55) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489556.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489556 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 6, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 7, 22, 22, 22, 18, 18, 7, 7, 7, 7, 16, 16, 24, 24, 24, 24, 7, 7, 7, 7, 4, 4, 4, 5, 5, 5, 4, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489556 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489556 Building ZINC001184489699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/56 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/57 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/58 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/58' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/59 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/59' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 Building ZINC001184489699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 56) grep: /scratch/xiaobo/236261/xbz-8058088.52/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[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 57) grep: /scratch/xiaobo/236261/xbz-8058088.52/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[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 58) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 59) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 Building ZINC001184489699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 56) grep: /scratch/xiaobo/236261/xbz-8058088.52/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[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 57) grep: /scratch/xiaobo/236261/xbz-8058088.52/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[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 58) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 59) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 Building ZINC001184489699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 56) grep: /scratch/xiaobo/236261/xbz-8058088.52/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[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 57) grep: /scratch/xiaobo/236261/xbz-8058088.52/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[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 58) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 17, 24, 24, 24, 24, 24, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 10, 10, 21, 21, 21, 19, 19, 10, 10, 10, 10, 17, 17, 24, 24, 24, 24, 10, 10, 10, 10, 5, 5, 5, 7, 7, 7, 5, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 59) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184489699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489699 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 10, 10, 10, 10, 10, 10, 10, 17, 22, 22, 22, 22, 22, 10, 10, 6, 2, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 10, 10, 10, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489699 Building ZINC001184489780 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489780 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/60 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489780 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 14, 35, 39, 39, 39, 39, 39, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 35, 35, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/61 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489780 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 14, 37, 43, 43, 43, 43, 43, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 37, 37, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 2] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489780 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 Building ZINC001184489780 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489780 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 60) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489780 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 14, 35, 39, 39, 39, 39, 39, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 35, 35, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 61) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489780 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 14, 37, 43, 43, 43, 43, 43, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 37, 37, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 2] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489780 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489780 Building ZINC001184489786 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489786 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/62 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489786 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 12, 31, 37, 37, 37, 37, 37, 5, 5, 5, 4, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 31, 31, 37, 37, 37, 37, 5, 5, 5, 5, 5, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/63 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489786 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 14, 37, 41, 41, 41, 41, 41, 6, 6, 6, 4, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 37, 37, 41, 41, 41, 41, 6, 6, 6, 6, 6, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489786 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 Building ZINC001184489786 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489786 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 62) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489786 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 12, 31, 37, 37, 37, 37, 37, 5, 5, 5, 4, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 31, 31, 37, 37, 37, 37, 5, 5, 5, 5, 5, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 63) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1) `ZINC001184489786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489786 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](OCc5csc(C)n5)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 14, 37, 41, 41, 41, 41, 41, 6, 6, 6, 4, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 37, 37, 41, 41, 41, 41, 6, 6, 6, 6, 6, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489786 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489786 Building ZINC001184489791 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489791 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/64 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1) `ZINC001184489791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489791 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 5, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 15, 24, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 24, 24, 44, 44, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/65 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1) `ZINC001184489791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489791 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 5, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 13, 25, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 25, 25, 33, 33, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489791 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 Building ZINC001184489791 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489791 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 64) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1) `ZINC001184489791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489791 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 5, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 15, 24, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 24, 24, 44, 44, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 65) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1) `ZINC001184489791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489791 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H]3CC[C@H]4COCc3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 5, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 13, 25, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 25, 25, 33, 33, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489791 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489791 Building ZINC001184489793 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489793 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/66 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1) `ZINC001184489793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489793 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 19, 29, 43, 43, 43, 43, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 8, 8, 29, 29, 43, 43, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/67 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1) `ZINC001184489793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489793 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 16, 30, 38, 38, 38, 38, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 5, 5, 30, 30, 38, 38, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489793 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 Building ZINC001184489793 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489793 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 66) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1) `ZINC001184489793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489793 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 19, 29, 43, 43, 43, 43, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 8, 8, 29, 29, 43, 43, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 67) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1) `ZINC001184489793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489793 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 16, 30, 38, 38, 38, 38, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 5, 5, 30, 30, 38, 38, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489793 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489793 Building ZINC001184489794 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489794 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/68 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489794 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 16, 32, 41, 41, 41, 41, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 8, 8, 32, 32, 41, 41, 4, 4, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/69 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489794 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 18, 37, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 37, 37, 43, 43, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489794 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 Building ZINC001184489794 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489794 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 68) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489794 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 16, 32, 41, 41, 41, 41, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 8, 8, 32, 32, 41, 41, 4, 4, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 69) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489794 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 18, 37, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 37, 37, 43, 43, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489794 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489794 Building ZINC001184489795 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489795 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/70 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489795 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 24, 35, 35, 35, 35, 35, 5, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 14, 14, 35, 35, 35, 35, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/71 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489795 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 24, 33, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 16, 16, 33, 33, 34, 34, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489795 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 Building ZINC001184489795 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489795 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 70) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489795 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 24, 35, 35, 35, 35, 35, 5, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 14, 14, 35, 35, 35, 35, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 71) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1) `ZINC001184489795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489795 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@H]4[C@@H](COCc5nccs5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 5, 12, 5, 1, 8, 1, 1, 14, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 24, 33, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 16, 16, 33, 33, 34, 34, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489795 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489795 Building ZINC001184489958 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489958 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/72 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489958 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 14, 14, 2, 5, 5, 5, 5, 5, 5, 12, 12, 20, 21, 21, 21, 5, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 112 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/73 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489958 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 9, 9, 12, 12, 2, 5, 5, 5, 5, 5, 5, 12, 12, 24, 25, 25, 25, 5, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 104 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489958 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 Building ZINC001184489958 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489958 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 72) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489958 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 2, 3, 9, 9, 14, 14, 2, 5, 5, 5, 5, 5, 5, 12, 12, 20, 21, 21, 21, 5, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 112 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 73) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489958 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 9, 9, 12, 12, 2, 5, 5, 5, 5, 5, 5, 12, 12, 24, 25, 25, 25, 5, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 104 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489958 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489958 Building ZINC001184489959 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489959 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/74 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489959 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 6, 6, 7, 7, 4, 5, 5, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 4, 4, 6, 6, 6, 4, 4, 4, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/75 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489959 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 6, 6, 8, 8, 4, 5, 5, 5, 5, 5, 5, 10, 10, 17, 17, 17, 17, 5, 4, 4, 7, 7, 7, 4, 4, 4, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489959 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 Building ZINC001184489959 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489959 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 74) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489959 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 6, 6, 7, 7, 4, 5, 5, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 4, 4, 6, 6, 6, 4, 4, 4, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 75) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184489959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184489959 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]3CCCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 6, 6, 8, 8, 4, 5, 5, 5, 5, 5, 5, 10, 10, 17, 17, 17, 17, 5, 4, 4, 7, 7, 7, 4, 4, 4, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184489959 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184489959 Building ZINC001184490076 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490076 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/76 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1) `ZINC001184490076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490076 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 12, 35, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 35, 35, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/77 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1) `ZINC001184490076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490076 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 10, 29, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 29, 29, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490076 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 Building ZINC001184490076 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490076 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 76) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1) `ZINC001184490076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490076 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 12, 35, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 35, 35, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 77) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1) `ZINC001184490076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490076 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](OCc4csc(C)n4)[C@H]4OCCC[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 14, 1, 5, 8, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 10, 29, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 29, 29, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490076 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490076 Building ZINC001184490199 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490199 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/78 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490199 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 6, 8, 8, 8, 8, 8, 8, 8, 22, 35, 35, 35, 35, 35, 35, 8, 8, 8, 6, 4, 4, 5, 5, 5, 4, 4, 4, 8, 8, 8, 8, 8, 8, 35, 35, 35, 8, 8, 8, 8, 8, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/79 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490199 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 18, 32, 32, 32, 32, 32, 32, 6, 6, 6, 4, 4, 4, 5, 5, 5, 4, 4, 4, 6, 6, 6, 6, 6, 6, 32, 32, 32, 6, 6, 6, 6, 6, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490199 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 Building ZINC001184490199 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490199 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 78) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490199 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 6, 8, 8, 8, 8, 8, 8, 8, 22, 35, 35, 35, 35, 35, 35, 8, 8, 8, 6, 4, 4, 5, 5, 5, 4, 4, 4, 8, 8, 8, 8, 8, 8, 35, 35, 35, 8, 8, 8, 8, 8, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 79) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490199 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 18, 32, 32, 32, 32, 32, 32, 6, 6, 6, 4, 4, 4, 5, 5, 5, 4, 4, 4, 6, 6, 6, 6, 6, 6, 32, 32, 32, 6, 6, 6, 6, 6, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490199 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490199 Building ZINC001184490200 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490200 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/80 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490200 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 38, 38, 38, 38, 38, 38, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 38, 38, 38, 9, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/81 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490200 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 23, 33, 33, 33, 33, 33, 33, 7, 7, 7, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 33, 33, 33, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490200 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 Building ZINC001184490200 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490200 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 80) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490200 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 38, 38, 38, 38, 38, 38, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 38, 38, 38, 9, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 81) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1) `ZINC001184490200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184490200 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(C[C@@H](Oc5ncccc5F)CO4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 23, 33, 33, 33, 33, 33, 33, 7, 7, 7, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 33, 33, 33, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490200 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490200 Building ZINC001184490141 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490141 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/82 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/83 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/84 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/84' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/85 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/85' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490141 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 Building ZINC001184490141 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490141 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 82) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 83) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 84) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 85) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490141 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 Building ZINC001184490141 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490141 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 82) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 83) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 84) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 85) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490141 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 Building ZINC001184490141 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490141 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 82) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 83) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 84) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 7, 8, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 35, 20, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 35, 35, 35, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 85) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1) `ZINC001184490141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184490141 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCN(c4cc(Cl)nc(SC)n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 36, 20, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 9, 9, 9, 9, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490141 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490141 Building ZINC001184490236 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490236 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/86 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1) `ZINC001184490236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490236 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 26, 29, 29, 26, 29, 29, 8, 8, 8, 8, 3, 3, 5, 5, 5, 3, 3, 3, 8, 8, 8, 8, 11, 26, 26, 29, 29, 26, 29, 29, 8, 8, 8, 8, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/87 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1) `ZINC001184490236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490236 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 3, 5, 7, 7, 7, 7, 7, 7, 10, 10, 10, 24, 27, 27, 24, 27, 27, 7, 7, 7, 7, 3, 3, 5, 5, 5, 3, 3, 3, 7, 7, 7, 7, 10, 24, 24, 27, 27, 24, 27, 27, 7, 7, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490236 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 Building ZINC001184490236 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490236 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 86) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1) `ZINC001184490236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490236 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 26, 29, 29, 26, 29, 29, 8, 8, 8, 8, 3, 3, 5, 5, 5, 3, 3, 3, 8, 8, 8, 8, 11, 26, 26, 29, 29, 26, 29, 29, 8, 8, 8, 8, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 87) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1) `ZINC001184490236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490236 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4nc(C(=O)NCc5ccccc5)sc4CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 3, 5, 7, 7, 7, 7, 7, 7, 10, 10, 10, 24, 27, 27, 24, 27, 27, 7, 7, 7, 7, 3, 3, 5, 5, 5, 3, 3, 3, 7, 7, 7, 7, 10, 24, 24, 27, 27, 24, 27, 27, 7, 7, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490236 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490236 Building ZINC001184490319 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490319 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/88 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490319 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 23, 23, 9, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/89 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490319 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 21, 21, 21, 21, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490319 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 Building ZINC001184490319 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490319 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 88) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490319 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 23, 23, 9, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 89) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490319 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 21, 21, 21, 21, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490319 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490319 Building ZINC001184490323 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490323 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/90 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490323 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 22, 22, 22, 22, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/91 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490323 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 10, 5, 5, 5, 5, 5, 5, 5, 5, 4, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490323 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 Building ZINC001184490323 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490323 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 90) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490323 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 22, 22, 22, 22, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 91) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1) `ZINC001184490323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490323 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@]3(C(F)(F)F)CCN(C(=O)OC(C)(C)C)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 10, 5, 5, 5, 5, 5, 5, 5, 5, 4, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490323 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490323 Building ZINC001184490303 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490303 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/92 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1) `ZINC001184490303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490303 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 6, 25, 25, 25, 25, 25, 25, 37, 37, 37, 37, 37, 25, 25, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 25, 25, 25, 25, 37, 37, 37, 37, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/93 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1) `ZINC001184490303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490303 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 4, 8, 24, 24, 26, 26, 26, 26, 35, 35, 35, 35, 35, 26, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 26, 26, 26, 26, 35, 35, 35, 35, 26, 26, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490303 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 Building ZINC001184490303 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490303 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 92) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1) `ZINC001184490303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490303 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 6, 25, 25, 25, 25, 25, 25, 37, 37, 37, 37, 37, 25, 25, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 25, 25, 25, 25, 37, 37, 37, 37, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 93) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1) `ZINC001184490303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490303 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(=O)N4CCN(c5ccccn5)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 4, 8, 24, 24, 26, 26, 26, 26, 35, 35, 35, 35, 35, 26, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 26, 26, 26, 26, 35, 35, 35, 35, 26, 26, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490303 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490303 Building ZINC001184490339 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490339 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/94 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1) `ZINC001184490339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490339 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 14, 27, 42, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 14, 14, 42, 42, 47, 47, 47, 47, 4, 4, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/95 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1) `ZINC001184490339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490339 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 14, 28, 44, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 14, 14, 44, 44, 50, 50, 50, 50, 4, 4, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490339 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 Building ZINC001184490339 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490339 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 94) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1) `ZINC001184490339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490339 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 14, 27, 42, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 14, 14, 42, 42, 47, 47, 47, 47, 4, 4, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 95) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1) `ZINC001184490339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490339 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(COCc5ccccn5)cncc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 14, 28, 44, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 14, 14, 44, 44, 50, 50, 50, 50, 4, 4, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490339 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490339 Building ZINC001184490385 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490385 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/96 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490385 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 10, 16, 16, 17, 17, 17, 17, 17, 17, 28, 28, 30, 31, 31, 31, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/97 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490385 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 21, 21, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490385 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 Building ZINC001184490385 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490385 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 96) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490385 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 10, 16, 16, 17, 17, 17, 17, 17, 17, 28, 28, 30, 31, 31, 31, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 97) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490385 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 21, 21, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490385 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490385 Building ZINC001184490386 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490386 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/98 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490386 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 12, 21, 23, 24, 24, 24, 24, 24, 24, 31, 31, 32, 32, 32, 32, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 3, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 24, 24, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/99 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490386 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 18, 19, 20, 20, 20, 20, 20, 20, 28, 28, 32, 32, 32, 32, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 20, 20, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490386 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 Building ZINC001184490386 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490386 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 98) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490386 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 12, 21, 23, 24, 24, 24, 24, 24, 24, 31, 31, 32, 32, 32, 32, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 3, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 24, 24, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 99) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1) `ZINC001184490386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490386 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCC4(CCN(C(=O)OC(C)(C)C)CC4)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 18, 19, 20, 20, 20, 20, 20, 20, 28, 28, 32, 32, 32, 32, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 20, 20, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490386 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490386 Building ZINC001184490552 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490552 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/100 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1) `ZINC001184490552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490552 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 25, 25, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/101 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1) `ZINC001184490552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490552 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 25, 25, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490552 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 Building ZINC001184490552 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490552 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 100) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1) `ZINC001184490552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490552 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 25, 25, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 101) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1) `ZINC001184490552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490552 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc4cccc5c4c(c3)C(=O)N(CCN(C)C)C5=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 25, 25, 26, 26, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490552 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490552 Building ZINC001184490517 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490517 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/102 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1) `ZINC001184490517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490517 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 5, 5, 10, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 14, 14, 14, 16, 16, 14, 14, 14, 14, 14, 14, 3, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/103 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1) `ZINC001184490517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490517 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 5, 5, 10, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 7, 13, 13, 13, 16, 16, 13, 13, 13, 13, 13, 13, 4, 8, 8, 8, 8, 5, 5, 7, 7, 7, 5, 5, 5, 7, 7, 16, 16, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 13, 13, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490517 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 Building ZINC001184490517 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490517 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 102) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1) `ZINC001184490517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490517 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 5, 5, 10, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 14, 14, 14, 16, 16, 14, 14, 14, 14, 14, 14, 3, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 103) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1) `ZINC001184490517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184490517 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3nn(C(C)C)c4c3CCNC4)c3nccs3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 5, 5, 10, 5, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 7, 13, 13, 13, 16, 16, 13, 13, 13, 13, 13, 13, 4, 8, 8, 8, 8, 5, 5, 7, 7, 7, 5, 5, 5, 7, 7, 16, 16, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 13, 13, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490517 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490517 Building ZINC001184490779 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490779 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/104 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184490779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184490779 none COC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 9, 23, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8, 9, 23, 23, 23, 9, 9, 3, 8, 8, 8, 10, 10, 10, 8, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/105 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184490779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184490779 none COC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8, 9, 22, 22, 22, 9, 9, 3, 8, 8, 8, 10, 10, 10, 8, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490779 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 Building ZINC001184490779 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490779 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 104) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184490779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184490779 none COC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 9, 23, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8, 9, 23, 23, 23, 9, 9, 3, 8, 8, 8, 10, 10, 10, 8, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 105) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184490779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184490779 none COC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8, 9, 22, 22, 22, 9, 9, 3, 8, 8, 8, 10, 10, 10, 8, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490779 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490779 Building ZINC001184491046 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491046 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/106 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 10, 6, 6, 14, 16, 29, 29, 45, 45, 45, 45, 45, 45, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 10, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/107 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 29, 29, 45, 45, 45, 45, 45, 45, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/108 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/108' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/109 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/109' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491046 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 Building ZINC001184491046 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491046 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 106) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 10, 6, 6, 14, 16, 29, 29, 45, 45, 45, 45, 45, 45, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 10, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 107) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 29, 29, 45, 45, 45, 45, 45, 45, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 108) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 109) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491046 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 Building ZINC001184491046 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491046 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 106) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 10, 6, 6, 14, 16, 29, 29, 45, 45, 45, 45, 45, 45, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 10, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 107) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 29, 29, 45, 45, 45, 45, 45, 45, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 108) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 109) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491046 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 Building ZINC001184491046 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491046 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 106) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 10, 6, 6, 14, 16, 29, 29, 45, 45, 45, 45, 45, 45, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 10, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 107) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 29, 29, 45, 45, 45, 45, 45, 45, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 29, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 108) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 109) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1) `ZINC001184491046.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491046 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)c(OCCC[N@]4CC[N@@](C)CC4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 9, 5, 5, 13, 16, 30, 30, 46, 46, 46, 46, 46, 46, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 16, 16, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491046 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491046 Building ZINC001184490865 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490865 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/110 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490865 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 22, 38, 38, 38, 38, 38, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 38, 38, 38, 38, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/111 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490865 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 33, 33, 33, 33, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490865 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 Building ZINC001184490865 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490865 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 110) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490865 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 22, 38, 38, 38, 38, 38, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 38, 38, 38, 38, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 111) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490865 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 33, 33, 33, 33, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490865 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490865 Building ZINC001184490866 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490866 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/112 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490866 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 31, 31, 31, 31, 31, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 22, 31, 31, 31, 31, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/113 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490866 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 33, 33, 33, 33, 33, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 33, 33, 33, 33, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490866 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 Building ZINC001184490866 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490866 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 112) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490866 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 31, 31, 31, 31, 31, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 22, 31, 31, 31, 31, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 113) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1) `ZINC001184490866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490866 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CCN(Cc5csc(C)n5)C4=O)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 33, 33, 33, 33, 33, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 33, 33, 33, 33, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490866 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490866 Building ZINC001184490899 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490899 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/114 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490899 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 24, 24, 24, 24, 24, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 7, 7, 3, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/115 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490899 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 27, 27, 27, 27, 27, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 14, 14, 14, 14, 14, 10, 10, 5, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490899 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 Building ZINC001184490899 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490899 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 114) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490899 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 24, 24, 24, 24, 24, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 7, 7, 3, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 115) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490899 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 27, 27, 27, 27, 27, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 14, 14, 14, 14, 14, 10, 10, 5, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490899 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490899 Building ZINC001184490900 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490900 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/116 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490900 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 27, 27, 27, 27, 27, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 13, 13, 13, 13, 13, 9, 9, 5, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/117 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490900 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 27, 27, 27, 27, 27, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 13, 13, 13, 13, 13, 6, 6, 3, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 3] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490900 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 Building ZINC001184490900 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490900 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 116) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490900 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 27, 27, 27, 27, 27, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 13, 13, 13, 13, 13, 9, 9, 5, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 4, 4, 4, 5, 5, 5, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 117) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184490900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490900 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 27, 27, 27, 27, 27, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 13, 13, 13, 13, 13, 6, 6, 3, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 3] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184490900 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184490900 Building ZINC001184491138 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491138 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/118 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491138 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 25, 38, 39, 39, 39, 39, 39, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 16, 16, 38, 38, 39, 39, 39, 39, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/119 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491138 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 14, 24, 28, 28, 28, 28, 28, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 8, 8, 24, 24, 28, 28, 28, 28, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491138 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 Building ZINC001184491138 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491138 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 118) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491138 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 25, 38, 39, 39, 39, 39, 39, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 16, 16, 38, 38, 39, 39, 39, 39, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 119) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491138 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 14, 24, 28, 28, 28, 28, 28, 5, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 8, 8, 24, 24, 28, 28, 28, 28, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491138 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491138 Building ZINC001184491142 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491142 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/120 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491142 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 21, 34, 36, 36, 36, 36, 36, 8, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 14, 14, 34, 34, 36, 36, 36, 36, 8, 8, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/121 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491142 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 30, 34, 34, 34, 34, 34, 6, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 10, 30, 30, 34, 34, 34, 34, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491142 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 Building ZINC001184491142 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491142 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 120) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491142 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 21, 34, 36, 36, 36, 36, 36, 8, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 14, 14, 34, 34, 36, 36, 36, 36, 8, 8, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 121) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1) `ZINC001184491142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491142 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4ccnn4C[C@H](COCc4csc(C)n4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 30, 34, 34, 34, 34, 34, 6, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 10, 30, 30, 34, 34, 34, 34, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491142 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491142 Building ZINC001184491167 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491167 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/122 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/123 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/124 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/124' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/125 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/125' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491167 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 Building ZINC001184491167 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491167 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 122) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 123) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 124) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 125) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491167 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 Building ZINC001184491167 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491167 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 122) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 123) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 124) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 125) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491167 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 Building ZINC001184491167 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491167 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 122) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 123) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 26, 26, 26, 26, 26, 26, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 26, 26, 26, 26, 26, 26, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 124) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 125) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491167.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491167 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 23, 23, 23, 23, 23, 23, 9, 5, 5, 6, 6, 6, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 23, 23, 23, 23, 23, 23, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491167 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491167 Building ZINC001184491171 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491171 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/126 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/127 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/128 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/128' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/129 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/129' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491171 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 Building ZINC001184491171 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491171 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 126) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 127) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 128) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 129) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491171 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 Building ZINC001184491171 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491171 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 126) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 127) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 128) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 129) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491171 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 Building ZINC001184491171 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491171 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 126) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 127) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 27, 27, 27, 27, 27, 27, 12, 4, 4, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 27, 27, 27, 27, 27, 27, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 128) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 129) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1) `ZINC001184491171.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184491171 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(Cc3c(C)noc3C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 23, 23, 23, 23, 23, 23, 10, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 23, 23, 23, 23, 23, 23, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491171 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491171 Building ZINC001184491182 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491182 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/130 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1) `ZINC001184491182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184491182 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 36, 36, 36, 39, 39, 39, 39, 39, 9, 3, 3, 4, 4, 4, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 36, 39, 39, 39, 39, 39, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/131 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1) `ZINC001184491182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184491182 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 35, 35, 35, 38, 38, 38, 38, 38, 9, 3, 3, 4, 4, 4, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 35, 38, 38, 38, 38, 38, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491182 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 Building ZINC001184491182 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491182 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 130) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1) `ZINC001184491182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184491182 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 36, 36, 36, 39, 39, 39, 39, 39, 9, 3, 3, 4, 4, 4, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 36, 39, 39, 39, 39, 39, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 131) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1) `ZINC001184491182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184491182 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](CNC(=O)c3ccccc3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 35, 35, 35, 38, 38, 38, 38, 38, 9, 3, 3, 4, 4, 4, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 35, 38, 38, 38, 38, 38, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491182 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491182 Building ZINC001184491201 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491201 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/132 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1) `ZINC001184491201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491201 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 2, 2, 2, 5, 10, 21, 33, 33, 21, 33, 33, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 3, 5, 5, 21, 21, 33, 33, 21, 33, 33] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/133 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1) `ZINC001184491201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491201 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 13, 32, 36, 36, 32, 36, 36, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 32, 32, 36, 36, 32, 36, 36] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491201 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 Building ZINC001184491201 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491201 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 132) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1) `ZINC001184491201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491201 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 2, 2, 2, 5, 10, 21, 33, 33, 21, 33, 33, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 3, 5, 5, 21, 21, 33, 33, 21, 33, 33] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 133) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1) `ZINC001184491201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491201 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 13, 32, 36, 36, 32, 36, 36, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 32, 32, 36, 36, 32, 36, 36] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491201 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491201 Building ZINC001184491202 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491202 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/134 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1) `ZINC001184491202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491202 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 12, 30, 35, 35, 30, 35, 35, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 30, 30, 35, 35, 30, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/135 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1) `ZINC001184491202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491202 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 2, 2, 2, 6, 11, 23, 34, 34, 23, 34, 34, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 3, 6, 6, 23, 23, 34, 34, 23, 34, 34] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491202 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 Building ZINC001184491202 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491202 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 134) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1) `ZINC001184491202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491202 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 12, 30, 35, 35, 30, 35, 35, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 30, 30, 35, 35, 30, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 135) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1) `ZINC001184491202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491202 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 2, 2, 2, 6, 11, 23, 34, 34, 23, 34, 34, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 3, 6, 6, 23, 23, 34, 34, 23, 34, 34] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491202 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491202 Building ZINC001184491379 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491379 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/136 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 97 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/137 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 98 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/138 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/138' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 20, 20, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 20, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 105 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/139 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/139' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 19, 19, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 19, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 103 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491379 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 Building ZINC001184491379 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491379 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 136) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 97 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 137) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 98 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 138) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 20, 20, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 20, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 105 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 139) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 19, 19, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 19, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 103 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491379 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 Building ZINC001184491379 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491379 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 136) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 97 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 137) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 98 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 138) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 20, 20, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 20, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 105 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 139) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 19, 19, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 19, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 103 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491379 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 Building ZINC001184491379 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491379 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 136) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 97 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 137) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 98 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 138) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 20, 20, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 20, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 105 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 139) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1) `ZINC001184491379.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184491379 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC[N@@](C4CCN(C(=O)OC(C)(C)C)CC4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 19, 19, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 14, 14, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 19, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 103 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184491379 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184491379 Building ZINC001184492843 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492843 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/140 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184492843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184492843 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 11, 13, 13, 13, 13, 13, 13, 23, 23, 34, 34, 34, 34, 13, 13, 13, 6, 6, 7, 7, 7, 6, 6, 6, 3, 10, 10, 13, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/141 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184492843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184492843 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 6, 8, 8, 8, 8, 8, 8, 22, 22, 28, 28, 28, 28, 8, 8, 8, 4, 4, 6, 6, 6, 4, 4, 4, 3, 6, 6, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184492843 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 Building ZINC001184492843 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492843 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 140) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184492843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184492843 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 11, 13, 13, 13, 13, 13, 13, 23, 23, 34, 34, 34, 34, 13, 13, 13, 6, 6, 7, 7, 7, 6, 6, 6, 3, 10, 10, 13, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 141) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184492843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184492843 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ncn4c3CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 6, 8, 8, 8, 8, 8, 8, 22, 22, 28, 28, 28, 28, 8, 8, 8, 4, 4, 6, 6, 6, 4, 4, 4, 3, 6, 6, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184492843 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492843 Building ZINC001184492877 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492877 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/142 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492877 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 9, 9, 9, 7, 7, 7, 5, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/143 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492877 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 5, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184492877 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 Building ZINC001184492877 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492877 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 142) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492877 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 9, 9, 9, 7, 7, 7, 5, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 143) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492877 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 5, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184492877 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492877 Building ZINC001184492878 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492878 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/144 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492878 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 5, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/145 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492878 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 9, 9, 9, 7, 7, 7, 5, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184492878 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 Building ZINC001184492878 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492878 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 144) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492878 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 5, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 145) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1) `ZINC001184492878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184492878 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCS(=O)(=O)c4ccc(Br)cc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 9, 9, 9, 7, 7, 7, 5, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184492878 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184492878 Building ZINC001184493069 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493069 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/146 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493069 none COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 7, 7, 14, 14, 14, 14, 14, 21, 23, 23, 23, 14, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/147 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493069 none COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 3, 6, 6, 15, 15, 15, 15, 15, 21, 22, 22, 22, 15, 15, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493069 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 Building ZINC001184493069 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493069 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 146) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493069 none COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 7, 7, 14, 14, 14, 14, 14, 21, 23, 23, 23, 14, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 147) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493069 none COC(=O)[C@H](Cc1ccc(OC(C)(C)C)cc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 3, 6, 6, 15, 15, 15, 15, 15, 21, 22, 22, 22, 15, 15, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493069 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493069 Building ZINC001184493198 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493198 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/148 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1) `ZINC001184493198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493198 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 37, 37, 38, 38, 38, 38, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 38, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/149 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1) `ZINC001184493198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493198 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 27, 27, 31, 31, 31, 31, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493198 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 Building ZINC001184493198 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493198 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 148) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1) `ZINC001184493198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493198 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 37, 37, 38, 38, 38, 38, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 38, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 149) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1) `ZINC001184493198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493198 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4ccccc4N(CC(=O)OC(C)(C)C)C3=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 27, 27, 31, 31, 31, 31, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493198 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493198 Building ZINC001184493252 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493252 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/150 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1) `ZINC001184493252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493252 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 10, 10, 10, 23, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 10, 10, 23, 23, 37, 37, 37, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/151 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1) `ZINC001184493252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493252 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 11, 11, 23, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 11, 11, 23, 23, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493252 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 Building ZINC001184493252 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493252 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 150) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1) `ZINC001184493252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493252 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 10, 10, 10, 23, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 10, 10, 23, 23, 37, 37, 37, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 151) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1) `ZINC001184493252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493252 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 11, 11, 23, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 11, 11, 23, 23, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493252 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493252 Building ZINC001184493404 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493404 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/152 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493404 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 8, 8, 11, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/153 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493404 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 6, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 25, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493404 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 Building ZINC001184493404 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493404 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 152) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493404 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 8, 8, 11, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 153) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493404 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 6, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 25, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493404 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493404 Building ZINC001184493405 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493405 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/154 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493405 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 5, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/155 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493405 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 8, 8, 12, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 30, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493405 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 Building ZINC001184493405 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493405 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 154) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493405 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 5, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 155) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1) `ZINC001184493405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493405 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC3c4ccccc4-c4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 8, 8, 12, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 30, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493405 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493405 Building ZINC001184493481 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493481 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/156 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1) `ZINC001184493481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184493481 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 23, 23, 17, 23, 23, 6, 6, 8, 8, 8, 6, 6, 6, 6, 45, 16, 16, 23, 23, 23, 23, 23, 6] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/157 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1) `ZINC001184493481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184493481 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 24, 24, 19, 24, 24, 6, 6, 8, 8, 8, 6, 6, 6, 6, 48, 17, 17, 24, 24, 24, 24, 24, 6] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493481 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 Building ZINC001184493481 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493481 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 156) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1) `ZINC001184493481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184493481 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 23, 23, 17, 23, 23, 6, 6, 8, 8, 8, 6, 6, 6, 6, 45, 16, 16, 23, 23, 23, 23, 23, 6] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 157) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1) `ZINC001184493481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184493481 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Br)c(O)nc(=O)n3Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 24, 24, 19, 24, 24, 6, 6, 8, 8, 8, 6, 6, 6, 6, 48, 17, 17, 24, 24, 24, 24, 24, 6] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493481 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493481 Building ZINC001184493486 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493486 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/158 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493486 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 9, 14, 14, 14, 14, 14, 27, 27, 44, 44, 44, 44, 14, 14, 14, 14, 5, 5, 6, 6, 6, 5, 5, 5, 3, 9, 9, 14, 14, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/159 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493486 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 14, 14, 14, 14, 14, 31, 31, 34, 34, 34, 34, 14, 14, 14, 14, 4, 4, 6, 6, 6, 4, 4, 4, 4, 9, 9, 14, 14, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493486 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 Building ZINC001184493486 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493486 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 158) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493486 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 9, 14, 14, 14, 14, 14, 27, 27, 44, 44, 44, 44, 14, 14, 14, 14, 5, 5, 6, 6, 6, 5, 5, 5, 3, 9, 9, 14, 14, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 159) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493486 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 14, 14, 14, 14, 14, 31, 31, 34, 34, 34, 34, 14, 14, 14, 14, 4, 4, 6, 6, 6, 4, 4, 4, 4, 9, 9, 14, 14, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493486 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493486 Building ZINC001184493488 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493488 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/160 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493488 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 20, 20, 20, 20, 20, 30, 30, 31, 31, 31, 31, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/161 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493488 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 12, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 29, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493488 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 Building ZINC001184493488 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493488 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 160) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493488 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 20, 20, 20, 20, 20, 30, 30, 31, 31, 31, 31, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 161) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1) `ZINC001184493488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184493488 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]3CCN(C(=O)OC(C)(C)C)CC3(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 12, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 29, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493488 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493488 Building ZINC001184493558 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493558 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/162 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493558 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 24, 4, 4, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/163 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493558 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 28, 21, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493558 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 Building ZINC001184493558 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493558 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 162) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493558 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 24, 4, 4, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 163) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493558 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 28, 21, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493558 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493558 Building ZINC001184493559 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493559 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/164 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493559 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 24, 4, 4, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/165 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493559 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 29, 29, 29, 26, 4, 4, 4, 4, 4, 4, 4, 4, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493559 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 Building ZINC001184493559 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493559 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 164) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493559 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 24, 4, 4, 4, 4, 4, 4, 4, 4, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 165) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493559 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 29, 29, 29, 26, 4, 4, 4, 4, 4, 4, 4, 4, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493559 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493559 Building ZINC001184493560 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493560 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/166 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493560 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 19, 25, 25, 25, 24, 25, 25, 25, 25, 25, 29, 29, 32, 33, 33, 33, 25, 5, 5, 5, 5, 5, 5, 5, 5, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 25, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/167 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493560 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 5, 17, 22, 22, 22, 20, 22, 22, 22, 22, 22, 29, 29, 31, 31, 31, 31, 22, 4, 4, 4, 4, 4, 4, 4, 4, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 22, 22, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493560 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 Building ZINC001184493560 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493560 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 166) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493560 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 19, 25, 25, 25, 24, 25, 25, 25, 25, 25, 29, 29, 32, 33, 33, 33, 25, 5, 5, 5, 5, 5, 5, 5, 5, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 25, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 167) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493560 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CO[C@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 5, 17, 22, 22, 22, 20, 22, 22, 22, 22, 22, 29, 29, 31, 31, 31, 31, 22, 4, 4, 4, 4, 4, 4, 4, 4, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 22, 22, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493560 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493560 Building ZINC001184493561 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493561 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/168 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493561 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 32, 32, 32, 32, 32, 32, 22, 4, 4, 4, 4, 4, 4, 4, 4, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 22, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/169 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493561 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493561 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 Building ZINC001184493561 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493561 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 168) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493561 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 32, 32, 32, 32, 32, 32, 22, 4, 4, 4, 4, 4, 4, 4, 4, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 22, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 169) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184493561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184493561 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CO[C@@]4(C3)CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493561 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493561 Building ZINC001184493662 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493662 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/170 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1) `ZINC001184493662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493662 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 1, 1, 8, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 7, 9, 9, 9, 20, 20, 16, 16, 29, 20, 20, 9, 9, 9, 9, 9, 7, 9, 9, 9, 5, 5, 9, 9, 9, 5, 5, 5, 9, 20, 20, 29, 29, 29, 29, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/171 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1) `ZINC001184493662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493662 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 1, 1, 8, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 7, 10, 10, 10, 22, 22, 10, 16, 33, 22, 22, 10, 10, 10, 10, 10, 7, 9, 9, 9, 5, 5, 8, 8, 8, 5, 5, 5, 10, 22, 22, 33, 33, 33, 33, 22, 22, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493662 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 Building ZINC001184493662 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493662 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 170) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1) `ZINC001184493662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493662 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 1, 1, 8, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 7, 9, 9, 9, 20, 20, 16, 16, 29, 20, 20, 9, 9, 9, 9, 9, 7, 9, 9, 9, 5, 5, 9, 9, 9, 5, 5, 5, 9, 20, 20, 29, 29, 29, 29, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 171) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1) `ZINC001184493662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184493662 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3cc(c4ccc(CN)cc4)nn(C)c3=O)C(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 1, 1, 8, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 7, 10, 10, 10, 22, 22, 10, 16, 33, 22, 22, 10, 10, 10, 10, 10, 7, 9, 9, 9, 5, 5, 8, 8, 8, 5, 5, 5, 10, 22, 22, 33, 33, 33, 33, 22, 22, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493662 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493662 Building ZINC001184493788 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493788 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/172 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1) `ZINC001184493788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184493788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 12, 15, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 8, 8, 8, 5, 5, 5, 12, 12, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/173 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1) `ZINC001184493788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184493788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 5, 10, 11, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 9, 9, 9, 6, 6, 6, 10, 10, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493788 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 Building ZINC001184493788 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493788 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 172) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1) `ZINC001184493788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184493788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 6, 12, 15, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 8, 8, 8, 5, 5, 5, 12, 12, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 173) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1) `ZINC001184493788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184493788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CCN)c3nc4ccc(C)cc4n4c(C)cnc34)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 5, 10, 11, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 9, 9, 9, 6, 6, 6, 10, 10, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184493788 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184493788 Building ZINC001184494286 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494286 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/174 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1) `ZINC001184494286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184494286 none COC(=O)c1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 13, 16, 9, 16, 16, 9, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 9, 9, 5, 5, 5, 9, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/175 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1) `ZINC001184494286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184494286 none COC(=O)c1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 9, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 9, 9, 5, 5, 5, 9, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184494286 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 Building ZINC001184494286 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494286 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 174) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1) `ZINC001184494286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184494286 none COC(=O)c1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 13, 16, 9, 16, 16, 9, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 9, 9, 5, 5, 5, 9, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 175) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1) `ZINC001184494286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184494286 none COC(=O)c1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)[C@H]2CC[C@H](N)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 7, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 9, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 9, 9, 5, 5, 5, 9, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184494286 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184494286 Building ZINC001184477777 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477777 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/176 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(n2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184477777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184477777 none CC(=O)N1CCC(n2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 31, 31, 31, 17, 10, 10, 10, 10, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 33, 33, 33, 31, 31, 31, 31, 31, 10, 10, 4, 4, 4, 4, 4, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/177 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(n2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184477777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184477777 none CC(=O)N1CCC(n2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 31, 31, 31, 16, 11, 11, 11, 11, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 36, 36, 36, 31, 31, 31, 31, 31, 11, 11, 5, 4, 4, 4, 4, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184477777 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 Building ZINC001184477777 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477777 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 176) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(n2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184477777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184477777 none CC(=O)N1CCC(n2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 31, 31, 31, 17, 10, 10, 10, 10, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 33, 33, 33, 31, 31, 31, 31, 31, 10, 10, 4, 4, 4, 4, 4, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 177) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(n2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184477777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184477777 none CC(=O)N1CCC(n2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 31, 31, 31, 16, 11, 11, 11, 11, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 36, 36, 36, 31, 31, 31, 31, 31, 11, 11, 5, 4, 4, 4, 4, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184477777 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184477777 Building ZINC001184478557 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478557 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/178 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184478557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478557 none O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 20, 20, 41, 41, 41, 41, 41, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 20, 41, 41, 41, 41, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/179 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184478557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478557 none O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 12, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 12, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478557 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 Building ZINC001184478557 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478557 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 178) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184478557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478557 none O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 20, 20, 41, 41, 41, 41, 41, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 20, 41, 41, 41, 41, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 179) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184478557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478557 none O=C(Nc1cccnc1)[C@@H]1C[C@H]2OCC[C@H]2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 12, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 12, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478557 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478557 Building ZINC001184478640 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478640 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/180 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478640 none O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 28, 7, 7, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/181 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478640 none O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 16, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 16, 16, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478640 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 Building ZINC001184478640 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478640 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 180) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478640 none O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 28, 7, 7, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 181) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478640 none O=C(N1CCN(Cc2ccc3c(c2)OCO3)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 16, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 16, 16, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478640 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478640 Building ZINC001184478692 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478692 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/182 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/183 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/184 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/184' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/185 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/185' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478692 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 Building ZINC001184478692 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478692 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 182) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 183) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 184) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 185) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478692 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 Building ZINC001184478692 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478692 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 182) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 183) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 184) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 185) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478692 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 Building ZINC001184478692 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478692 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 182) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 183) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 29, 29, 29, 29, 29, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 184) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 185) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478692 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 21, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478692 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478692 Building ZINC001184478696 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478696 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/186 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/187 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/188 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/188' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/189 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/189' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478696 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 Building ZINC001184478696 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478696 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 186) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 187) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 188) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 189) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478696 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 Building ZINC001184478696 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478696 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 186) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 187) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 188) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 189) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478696 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 Building ZINC001184478696 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478696 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 186) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 187) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 18, 34, 34, 34, 34, 34, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 18, 18, 34, 34, 34, 34, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 188) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 189) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478696.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478696 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 22, 40, 40, 40, 40, 40, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478696 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478696 Building ZINC001184478699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/190 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/191 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/192 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/192' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/193 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/193' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 Building ZINC001184478699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 190) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 191) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 192) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 193) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 Building ZINC001184478699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 190) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 191) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 192) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 193) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 Building ZINC001184478699 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478699 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 190) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 191) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 11, 24, 42, 42, 42, 42, 42, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 192) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 193) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478699.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478699 none O=C(N1CCN2C[C@@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 17, 37, 37, 37, 37, 37, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 17, 17, 37, 37, 37, 37, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478699 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478699 Building ZINC001184478704 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478704 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/194 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/195 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/196 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/196' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/197 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/197' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478704 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 Building ZINC001184478704 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478704 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 194) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 195) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 196) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 197) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478704 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 Building ZINC001184478704 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478704 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 194) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 195) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 196) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 197) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478704 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 Building ZINC001184478704 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184478704 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 194) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 195) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 19, 39, 39, 39, 39, 39, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 196) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 197) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478704.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184478704 none O=C(N1CCN2C[C@H](OCc3cccnc3)C[C@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 7, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 30, 30, 30, 30, 30, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 16, 16, 30, 30, 30, 30, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478704 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478704 Building ZINC001184478748 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478748 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/198 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478748 none O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 26, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 26, 26, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/199 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478748 none O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 19, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 19, 19, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478748 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 Building ZINC001184478748 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478748 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 198) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478748 none O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 26, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 26, 26, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 199) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478748 none O=C(NCc1cccnc1)[C@@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 19, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 19, 19, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478748 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478748 Building ZINC001184478763 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478763 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/200 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478763 none O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 19, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 19, 19, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/201 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478763 none O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 24, 24, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478763 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 Building ZINC001184478763 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478763 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 200) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478763 none O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 19, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 19, 19, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 201) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478763 none O=C(NCc1cccnc1)[C@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 24, 24, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478763 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478763 Building ZINC001184478767 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478767 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/202 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478767 none O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 19, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 19, 19, 33, 33, 33, 33, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/203 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478767 none O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 29, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 29, 29, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478767 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 Building ZINC001184478767 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478767 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 202) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478767 none O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 19, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 19, 19, 33, 33, 33, 33, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 203) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478767 none O=C(NCc1cccnc1)[C@@H]1C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 29, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 29, 29, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478767 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478767 Building ZINC001184478771 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478771 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/204 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478771 none O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 29, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 29, 29, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/205 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478771 none O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 19, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 19, 19, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478771 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 Building ZINC001184478771 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478771 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 204) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478771 none O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 29, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 29, 29, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 205) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184478771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478771 none O=C(NCc1cccnc1)[C@H]1C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 19, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 19, 19, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478771 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478771 Building ZINC001184478786 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478786 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/206 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1) `ZINC001184478786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184478786 none O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 19, 22, 31, 31, 31, 13, 13, 7, 7, 7, 7, 5, 5, 5, 5, 7, 7, 7, 7, 19, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/207 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1) `ZINC001184478786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184478786 none O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 23, 25, 34, 34, 34, 15, 15, 6, 6, 6, 6, 3, 3, 3, 3, 6, 6, 6, 6, 23, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478786 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 Building ZINC001184478786 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478786 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 206) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1) `ZINC001184478786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184478786 none O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 19, 22, 31, 31, 31, 13, 13, 7, 7, 7, 7, 5, 5, 5, 5, 7, 7, 7, 7, 19, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 207) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1) `ZINC001184478786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184478786 none O=C(C[C@H]1OC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]21)NC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 23, 25, 34, 34, 34, 15, 15, 6, 6, 6, 6, 3, 3, 3, 3, 6, 6, 6, 6, 23, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478786 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478786 Building ZINC001184478809 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478809 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/208 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478809 none CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 15, 32, 43, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/209 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478809 none CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 18, 32, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 31, 31, 31, 32, 32, 32, 32, 32, 16, 16, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478809 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 Building ZINC001184478809 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478809 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 208) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478809 none CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 15, 32, 43, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 209) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478809 none CCN(CC)c1ccnc([C@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 18, 32, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 31, 31, 31, 32, 32, 32, 32, 32, 16, 16, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478809 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478809 Building ZINC001184478811 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478811 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/210 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478811 none CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 19, 17, 19, 33, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33, 17, 17, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/211 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478811 none CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 34, 46, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 23, 23, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478811 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 Building ZINC001184478811 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478811 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 210) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478811 none CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 19, 17, 19, 33, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33, 17, 17, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 211) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184478811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184478811 none CCN(CC)c1ccnc([C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 8, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 34, 46, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 23, 23, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478811 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478811 Building ZINC001184478813 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478813 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/212 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478813 none O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 5, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/213 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478813 none O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 20, 20, 20, 20, 20, 20, 20, 20, 6, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478813 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 Building ZINC001184478813 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478813 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 212) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478813 none O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 5, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 213) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184478813 none O=C(N(Cc1cn2c(n1)CNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 20, 20, 20, 20, 20, 20, 20, 20, 6, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478813 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478813 Building ZINC001184478860 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478860 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/214 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C) `ZINC001184478860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478860 none CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 17, 17, 17, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/215 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C) `ZINC001184478860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478860 none CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478860 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 Building ZINC001184478860 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478860 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 214) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C) `ZINC001184478860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478860 none CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 17, 17, 17, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 215) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C) `ZINC001184478860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478860 none CCN1C(=O)[C@]2(CC[C@@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@@H]32)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478860 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478860 Building ZINC001184478880 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478880 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/216 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478880 none CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 13, 15, 15, 15, 15, 21, 21, 24, 24, 24, 24, 15, 15, 15, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 8, 8, 15, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/217 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478880 none CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 19, 19, 19, 19, 28, 28, 32, 32, 32, 32, 19, 19, 19, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 19, 19, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 19, 19, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478880 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 Building ZINC001184478880 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478880 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 216) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478880 none CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 13, 15, 15, 15, 15, 21, 21, 24, 24, 24, 24, 15, 15, 15, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 8, 8, 15, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 217) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478880 none CN(C[C@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 19, 19, 19, 19, 28, 28, 32, 32, 32, 32, 19, 19, 19, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 19, 19, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 19, 19, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478880 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478880 Building ZINC001184478881 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478881 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/218 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478881 none CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 19, 19, 19, 19, 27, 27, 31, 31, 31, 31, 19, 19, 19, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/219 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478881 none CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 12, 14, 14, 14, 14, 20, 20, 24, 24, 24, 24, 14, 14, 14, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 8, 8, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478881 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 Building ZINC001184478881 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478881 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 218) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478881 none CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 19, 19, 19, 19, 27, 27, 31, 31, 31, 31, 19, 19, 19, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 19, 19, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 219) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478881 none CN(C[C@@H]1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 12, 14, 14, 14, 14, 20, 20, 24, 24, 24, 24, 14, 14, 14, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 8, 8, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184478881 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184478881 Building ZINC001184479232 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479232 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/220 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479232 none CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 16, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 7, 7, 7, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 16, 16, 7, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/221 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479232 none CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 9, 9, 9, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 23, 23, 9, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479232 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 Building ZINC001184479232 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479232 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 220) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479232 none CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 16, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 7, 7, 7, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 16, 16, 7, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 221) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479232 none CC(=O)NC[C@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 9, 9, 9, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 23, 23, 9, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479232 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479232 Building ZINC001184479235 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479235 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/222 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479235 none CC(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 22, 22, 9, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/223 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479235 none CC(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 17, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 17, 17, 8, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479235 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 Building ZINC001184479235 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479235 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 222) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479235 none CC(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 22, 22, 9, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 223) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184479235 none CC(=O)NC[C@@H]1c2ncn(C(C)C)c2CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 1, 8, 1, 8, 5, 5, 5, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 17, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 17, 17, 8, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479235 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479235 Building ZINC001184479238 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479238 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/224 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479238 none O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 11, 21, 24, 24, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 10, 10, 21, 21, 24, 24, 24, 24, 24, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/225 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479238 none O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 13, 21, 21, 21, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 10, 10, 21, 21, 21, 21, 21, 21, 21, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479238 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 Building ZINC001184479238 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479238 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 224) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479238 none O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 11, 21, 24, 24, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 10, 10, 21, 21, 24, 24, 24, 24, 24, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 225) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479238 none O=C(N1Cc2nccn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 13, 21, 21, 21, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 10, 10, 21, 21, 21, 21, 21, 21, 21, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479238 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479238 Building ZINC001184479239 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479239 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/226 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479239 none O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 22, 22, 22, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 10, 10, 22, 22, 22, 22, 22, 22, 22, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/227 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479239 none O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 21, 22, 22, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 8, 8, 21, 21, 22, 22, 22, 22, 22, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479239 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 Building ZINC001184479239 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479239 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 226) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479239 none O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 22, 22, 22, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 10, 10, 22, 22, 22, 22, 22, 22, 22, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 227) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479239 none O=C(N1Cc2nccn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 21, 22, 22, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 8, 8, 21, 21, 22, 22, 22, 22, 22, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479239 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479239 Building ZINC001184479240 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479240 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/228 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1) `ZINC001184479240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479240 none O=C(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 25, 26, 26, 25, 26, 26, 14, 14, 14, 14, 14, 14, 13, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 26, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/229 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1) `ZINC001184479240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479240 none O=C(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 13, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 14, 14, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479240 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 Building ZINC001184479240 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479240 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 228) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1) `ZINC001184479240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479240 none O=C(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 25, 26, 26, 25, 26, 26, 14, 14, 14, 14, 14, 14, 13, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 26, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 229) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1) `ZINC001184479240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479240 none O=C(c1ccccc1)N1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 13, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 14, 14, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479240 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479240 Building ZINC001184479242 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479242 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/230 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479242 none O=C(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 8, 1, 5, 15, 15, 15, 14, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/231 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479242 none O=C(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 8, 1, 5, 15, 15, 15, 14, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479242 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 Building ZINC001184479242 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479242 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 230) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479242 none O=C(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 8, 1, 5, 15, 15, 15, 14, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 231) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479242 none O=C(N1CCN(c2nnc(C(F)(F)F)s2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 8, 1, 5, 15, 15, 15, 14, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479242 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479242 Building ZINC001184479249 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479249 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/232 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479249 none O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 25, 25, 25, 25, 25, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/233 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479249 none O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 26, 26, 26, 26, 26, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479249 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 Building ZINC001184479249 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479249 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 232) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479249 none O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 25, 25, 25, 25, 25, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 233) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479249 none O=C(N1CC[C@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 26, 26, 26, 26, 26, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479249 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479249 Building ZINC001184479250 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479250 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/234 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479250 none O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 28, 28, 28, 28, 28, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/235 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479250 none O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 28, 28, 28, 28, 28, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479250 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 Building ZINC001184479250 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479250 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 234) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479250 none O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 28, 28, 28, 28, 28, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 235) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479250 none O=C(N1CC[C@@H](S(=O)(=O)c2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 7, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 28, 28, 28, 28, 28, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479250 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479250 Building ZINC001184479349 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479349 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/236 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184479349 none O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 8, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/237 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184479349 none O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 8, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479349 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 Building ZINC001184479349 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479349 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 236) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184479349 none O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 8, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 237) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184479349 none O=C(N1CCN(c2cccc3n[nH]cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 8, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479349 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479349 Building ZINC001184479426 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479426 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/238 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1cnc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1) `ZINC001184479426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184479426 none Nc1cnc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 18, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 7, 9, 9, 9, 9, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/239 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1) `ZINC001184479426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184479426 none Nc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 18, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 7, 9, 9, 9, 9, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479426 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 Building ZINC001184479426 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479426 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 238) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1cnc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1) `ZINC001184479426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184479426 none Nc1cnc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 18, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 7, 9, 9, 9, 9, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 239) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1) `ZINC001184479426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184479426 none Nc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(I)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 18, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 7, 9, 9, 9, 9, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479426 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479426 Building ZINC001184479397 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479397 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/240 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479397 none O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/241 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479397 none O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 17, 17, 17, 17, 17, 17, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479397 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 Building ZINC001184479397 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479397 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 240) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479397 none O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 241) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479397 none O=C(N(c1ncccc1F)[C@@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 17, 17, 17, 17, 17, 17, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479397 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479397 Building ZINC001184479398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/242 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479398 none O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 16, 16, 16, 16, 16, 16, 7, 15, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/243 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479398 none O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 15, 15, 15, 15, 15, 15, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 Building ZINC001184479398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 242) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479398 none O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 16, 16, 16, 16, 16, 16, 7, 15, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 243) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479398 none O=C(N(c1ncccc1F)[C@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 15, 15, 15, 15, 15, 15, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479398 Building ZINC001184479399 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479399 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/244 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479399 none O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 14, 14, 14, 14, 14, 14, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/245 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479399 none O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 17, 17, 17, 17, 17, 17, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479399 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 Building ZINC001184479399 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479399 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 244) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479399 none O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 14, 14, 14, 14, 14, 14, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 245) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479399 none O=C(N(c1ncccc1F)[C@H]1CO[C@@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 17, 17, 17, 17, 17, 17, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479399 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479399 Building ZINC001184479400 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479400 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/246 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479400 none O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 17, 17, 17, 17, 17, 17, 8, 14, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/247 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479400 none O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 16, 16, 16, 16, 16, 16, 7, 17, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479400 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 Building ZINC001184479400 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479400 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 246) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479400 none O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 17, 17, 17, 17, 17, 17, 8, 14, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 247) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479400 none O=C(N(c1ncccc1F)[C@@H]1CO[C@]2(CCNC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 5, 7, 5, 12, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 16, 16, 16, 16, 16, 16, 7, 17, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479400 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479400 Building ZINC001184479413 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479413 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/248 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479413 none O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 11, 8, 1, 1, 1, 14, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 11, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 11, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 24, 24, 24, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/249 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479413 none O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 11, 8, 1, 1, 1, 14, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 10, 10, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 19, 19, 19, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479413 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 Building ZINC001184479413 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479413 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 248) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479413 none O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 11, 8, 1, 1, 1, 14, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 11, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 11, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 24, 24, 24, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 249) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479413 none O=C(N1C[C@@H]2C(=O)N(c3ccsc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 11, 8, 1, 1, 1, 14, 1, 5, 5, 7, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 10, 10, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 19, 19, 19, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479413 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479413 Building ZINC001184479440 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479440 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/250 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/251 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/252 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/252' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/253 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/253' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479440 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 Building ZINC001184479440 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479440 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 250) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 251) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 252) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 253) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479440 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 Building ZINC001184479440 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479440 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 250) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 251) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 252) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 253) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479440 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 Building ZINC001184479440 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479440 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 250) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 251) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 252) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 253) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479440.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184479440 none O=C(N1CC[C@H]2[C@H]1CCN2Cc1cccnc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 24, 24, 24, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479440 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479440 Building ZINC001184479469 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479469 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/254 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1oc2nccnc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479469 none CCOC(=O)c1oc2nccnc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 11, 26, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 11, 11, 4, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/255 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1oc2nccnc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479469 none CCOC(=O)c1oc2nccnc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 11, 25, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 11, 11, 4, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479469 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 Building ZINC001184479469 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479469 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 254) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1oc2nccnc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479469 none CCOC(=O)c1oc2nccnc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 11, 26, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 11, 11, 4, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 255) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1oc2nccnc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184479469 none CCOC(=O)c1oc2nccnc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 3, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 11, 25, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 11, 11, 4, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479469 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479469 Building ZINC001184479461 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479461 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/256 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/257 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/258 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/258' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/259 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/259' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479461 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 Building ZINC001184479461 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479461 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 256) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 257) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 258) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 259) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479461 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 Building ZINC001184479461 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479461 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 256) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 257) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 258) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 259) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479461 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 Building ZINC001184479461 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479461 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 256) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 257) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 23, 35, 35, 35, 35, 35, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 23, 23, 35, 35, 35, 35, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 258) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 259) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12) `ZINC001184479461.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479461 none CN(Cc1cccnc1)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 25, 25, 25, 25, 25, 11, 11, 11, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 14, 14, 25, 25, 25, 25, 11, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479461 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479461 Building ZINC001184479466 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479466 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/260 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184479466 none O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 20, 29, 29, 29, 29, 13, 13, 13, 13, 13, 13, 4, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 29, 29, 29, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/261 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184479466 none O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 29, 29, 29, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479466 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 Building ZINC001184479466 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479466 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 260) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184479466 none O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 20, 29, 29, 29, 29, 13, 13, 13, 13, 13, 13, 4, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 29, 29, 29, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 261) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184479466 none O=C(c1ccco1)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 29, 29, 29, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479466 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479466 Building ZINC001184479506 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479506 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/262 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479506 none C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 27, 12, 27, 10, 10, 10, 10, 10, 10, 10, 4, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/263 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479506 none C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 9, 28, 9, 9, 9, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479506 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 Building ZINC001184479506 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479506 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 262) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479506 none C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 27, 12, 27, 10, 10, 10, 10, 10, 10, 10, 4, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 263) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479506 none C[C@@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 9, 28, 9, 9, 9, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479506 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479506 Building ZINC001184479881 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479881 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/264 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479881 none C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 9, 28, 9, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/265 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479881 none C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 29, 10, 29, 10, 10, 10, 10, 10, 10, 10, 4, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479881 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 Building ZINC001184479881 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479881 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 264) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479881 none C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 9, 28, 9, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 265) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184479881 none C[C@H]1CCCN1C(=O)c1n[nH]c2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 29, 10, 29, 10, 10, 10, 10, 10, 10, 10, 4, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479881 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479881 Building ZINC001184479941 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479941 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/266 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479941 none O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 31, 31, 31, 31, 31, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 20, 20, 31, 31, 31, 31, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/267 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479941 none O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 23, 23, 23, 23, 23, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 23, 23, 23, 23, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479941 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 Building ZINC001184479941 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479941 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 266) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479941 none O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 31, 31, 31, 31, 31, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 20, 20, 31, 31, 31, 31, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 267) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184479941 none O=C(N1CCCn2nnc(COc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 23, 23, 23, 23, 23, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 23, 23, 23, 23, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479941 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479941 Building ZINC001184479989 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479989 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/268 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184479989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184479989 none O=C(Nc1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 27, 32, 33, 33, 32, 33, 33, 16, 16, 16, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 32, 33, 33, 32, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/269 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184479989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184479989 none O=C(Nc1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 25, 34, 34, 34, 34, 34, 34, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 34, 34, 34, 34, 34, 34, 17, 17, 17, 17, 4, 4, 4, 4, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479989 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 Building ZINC001184479989 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479989 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 268) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184479989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184479989 none O=C(Nc1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 27, 32, 33, 33, 32, 33, 33, 16, 16, 16, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 32, 33, 33, 32, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 269) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184479989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184479989 none O=C(Nc1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 25, 34, 34, 34, 34, 34, 34, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 34, 34, 34, 34, 34, 34, 17, 17, 17, 17, 4, 4, 4, 4, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184479989 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184479989 Building ZINC001184480002 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480002 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/270 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184480002 none O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 5, 5, 5, 5, 5, 22, 25, 25, 23, 25, 25, 25, 5, 5, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 22, 22, 25, 25, 25, 25, 5, 5, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/271 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184480002 none O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 7, 7, 7, 7, 7, 30, 32, 32, 31, 32, 32, 32, 7, 7, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 30, 30, 32, 32, 32, 32, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480002 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 Building ZINC001184480002 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480002 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 270) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184480002 none O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 5, 5, 5, 5, 5, 22, 25, 25, 23, 25, 25, 25, 5, 5, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 22, 22, 25, 25, 25, 25, 5, 5, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 271) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184480002 none O=C(N1CCn2c(Cc3ccc(F)cc3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 7, 7, 7, 7, 7, 30, 32, 32, 31, 32, 32, 32, 7, 7, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 30, 30, 32, 32, 32, 32, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480002 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480002 Building ZINC001184480038 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480038 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/272 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480038 none O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 6, 9, 15, 15, 9, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/273 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480038 none O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 6, 10, 15, 15, 11, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480038 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 Building ZINC001184480038 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480038 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 272) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480038 none O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 6, 9, 15, 15, 9, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 273) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480038 none O=C(N(Cc1cnc2n1CCNCC2)c1ccccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 6, 10, 15, 15, 11, 15, 15, 15, 15, 15, 4, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480038 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480038 Building ZINC001184480075 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480075 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/274 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480075 none O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 18, 38, 38, 38, 38, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/275 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480075 none O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 18, 41, 41, 41, 41, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480075 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 Building ZINC001184480075 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480075 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 274) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480075 none O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 18, 38, 38, 38, 38, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 275) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480075 none O=C(Nc1cccnc1)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 18, 41, 41, 41, 41, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480075 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480075 Building ZINC001184480096 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480096 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/276 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480096 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/277 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480096 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480096 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 Building ZINC001184480096 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480096 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 276) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480096 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 277) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480096 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480096 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480096 Building ZINC001184480098 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480098 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/278 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480098 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/279 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480098 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480098 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 Building ZINC001184480098 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480098 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 278) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480098 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 279) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1) `ZINC001184480098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480098 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480098 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480098 Building ZINC001184480100 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480100 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/280 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480100 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 20, 20, 17, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/281 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480100 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 23, 23, 18, 23, 23, 23, 23, 23, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480100 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 Building ZINC001184480100 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480100 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 280) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480100 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 20, 20, 17, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 281) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480100 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 23, 23, 18, 23, 23, 23, 23, 23, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480100 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480100 Building ZINC001184480102 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480102 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/282 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480102 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/283 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480102 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480102 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 Building ZINC001184480102 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480102 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 282) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480102 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 283) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1) `ZINC001184480102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480102 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CO[C@@]3(C2)CCCNC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 5, 10, 5, 8, 8, 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, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480102 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480102 Building ZINC001184480178 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480178 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/284 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1) `ZINC001184480178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480178 none Nc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 16, 16, 16, 16, 48, 16, 16, 16, 16, 17] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/285 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1) `ZINC001184480178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480178 none Nc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 16, 16, 16, 16, 48, 16, 16, 16, 16, 17] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480178 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 Building ZINC001184480178 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480178 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 284) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Nc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1) `ZINC001184480178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480178 none Nc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 16, 16, 16, 16, 48, 16, 16, 16, 16, 17] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 285) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Nc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1) `ZINC001184480178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480178 none Nc1ccc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@H]2CC[C@H](O)CC2)nc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 16, 16, 16, 16, 48, 16, 16, 16, 16, 17] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480178 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480178 Building ZINC001184480179 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480179 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/286 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1) `ZINC001184480179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480179 none Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/287 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1) `ZINC001184480179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480179 none Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 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: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480179 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 Building ZINC001184480179 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480179 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 286) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1) `ZINC001184480179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480179 none Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 287) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1) `ZINC001184480179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480179 none Cc1noc([C@@H]2CC[C@@H]3[C@@H](CCN3C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 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: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480179 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480179 Building ZINC001184480391 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480391 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/288 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480391 none O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 14, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/289 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480391 none O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 3, 15, 31, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480391 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 Building ZINC001184480391 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480391 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 288) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480391 none O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 14, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 289) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480391 none O=C(N1C[C@H](Oc2cccnc2)[C@H]2OCCC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 3, 15, 31, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480391 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480391 Building ZINC001184480203 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480203 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/290 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1) `ZINC001184480203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184480203 none O=C(Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 23, 28, 28, 25, 28, 28, 13, 13, 3, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/291 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1) `ZINC001184480203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184480203 none O=C(Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 23, 28, 28, 25, 28, 28, 13, 13, 3, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480203 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 Building ZINC001184480203 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480203 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 290) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1) `ZINC001184480203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184480203 none O=C(Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 23, 28, 28, 25, 28, 28, 13, 13, 3, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 291) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1) `ZINC001184480203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184480203 none O=C(Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n[nH]1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 23, 28, 28, 25, 28, 28, 13, 13, 3, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480203 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480203 Building ZINC001184480412 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480412 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/292 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1) `ZINC001184480412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480412 none CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 29, 16, 9, 16, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/293 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1) `ZINC001184480412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480412 none CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 14, 8, 14, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480412 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 Building ZINC001184480412 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480412 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 292) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1) `ZINC001184480412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480412 none CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 29, 16, 9, 16, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 293) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1) `ZINC001184480412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480412 none CC(C)(C)OC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCO[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 14, 8, 14, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480412 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480412 Building ZINC001184480428 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480428 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/294 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480428 none CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/295 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480428 none CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 29, 29, 29, 29, 29, 29, 29, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480428 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 Building ZINC001184480428 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480428 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 294) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480428 none CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 295) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480428 none CC(C)C(=O)N[C@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 29, 29, 29, 29, 29, 29, 29, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480428 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480428 Building ZINC001184480429 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480429 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/296 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480429 none CC(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 28, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 28, 28, 28, 28, 28, 28, 28, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/297 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480429 none CC(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 17, 17, 17, 17] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480429 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 Building ZINC001184480429 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480429 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 296) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480429 none CC(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 28, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 28, 28, 28, 28, 28, 28, 28, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 297) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480429 none CC(C)C(=O)N[C@@H]1COCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 17, 17, 17, 17] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480429 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480429 Building ZINC001184480433 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480433 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/298 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/299 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/300 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/300' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/301 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/301' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480433 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 Building ZINC001184480433 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480433 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 298) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 299) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 300) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 301) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480433 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 Building ZINC001184480433 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480433 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 298) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 299) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 300) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 301) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480433 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 Building ZINC001184480433 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480433 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 298) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 299) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 300) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 301) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480433.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480433 none CC(C)N(C)Cc1[nH]nc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 8, 6, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 5, 5, 5, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480433 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480433 Building ZINC001184480462 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480462 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/302 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480462 none O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 11, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/303 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480462 none O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480462 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 Building ZINC001184480462 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480462 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 302) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480462 none O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 11, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 303) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480462 none O=C(N1CCC2(C[C@@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 10, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480462 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480462 Building ZINC001184480464 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480464 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/304 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480464 none O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 11, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/305 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480464 none O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480464 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 Building ZINC001184480464 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480464 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 304) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480464 none O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 11, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 305) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480464 none O=C(N1CCC2(C[C@H](c3cccnc3)C(=O)N2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480464 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480464 Building ZINC001184480474 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480474 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/306 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480474 none O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 12, 21, 31, 31, 31, 31, 31, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/307 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480474 none O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 23, 32, 32, 32, 32, 32, 4, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 23, 23, 32, 32, 32, 32, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480474 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 Building ZINC001184480474 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480474 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 306) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480474 none O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 12, 21, 31, 31, 31, 31, 31, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 307) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480474 none O=C(N1CCO[C@H]2[C@H](OCc3ccncc3)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 23, 32, 32, 32, 32, 32, 4, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 23, 23, 32, 32, 32, 32, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480474 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480474 Building ZINC001184480478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/308 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/309 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/310 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/310' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/311 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/311' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 Building ZINC001184480478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 308) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 309) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 310) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 311) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 Building ZINC001184480478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 308) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 309) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 310) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 311) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 Building ZINC001184480478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 308) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 309) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 17, 28, 28, 28, 28, 28, 8, 8, 8, 11, 11, 11, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 17, 17, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 310) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 311) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21) `ZINC001184480478.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480478 none CO[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2CN(Cc3cccnc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 16, 16, 27, 27, 27, 27, 6, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480478 Building ZINC001184480484 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480484 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/312 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480484 none O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 31, 31, 31, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 28, 28, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/313 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480484 none O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 31, 31, 31, 31, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 28, 28, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480484 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 Building ZINC001184480484 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480484 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 312) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480484 none O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 31, 31, 31, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 28, 28, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 313) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480484 none O=C(NCc1ccco1)C12CC(C1)CN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 31, 31, 31, 31, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 28, 28, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480484 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480484 Building ZINC001184480538 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480538 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/314 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480538 none CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 20, 10, 10, 10, 10, 10, 10, 10, 16, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 20, 20, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/315 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480538 none CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 22, 7, 7, 7, 7, 7, 7, 7, 11, 7, 7, 7, 7, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 33, 33, 33, 33, 33, 22, 22, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480538 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 Building ZINC001184480538 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480538 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 314) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480538 none CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 20, 10, 10, 10, 10, 10, 10, 10, 16, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 20, 20, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 315) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480538 none CCOC[C@@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 22, 7, 7, 7, 7, 7, 7, 7, 11, 7, 7, 7, 7, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 33, 33, 33, 33, 33, 22, 22, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480538 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480538 Building ZINC001184480539 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480539 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/316 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480539 none CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 20, 7, 7, 7, 7, 7, 7, 7, 11, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 28, 28, 28, 28, 28, 20, 20, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 7, 7, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/317 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480539 none CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 21, 10, 10, 10, 10, 10, 10, 10, 15, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 32, 32, 32, 32, 32, 21, 21, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480539 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 Building ZINC001184480539 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480539 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 316) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480539 none CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 20, 7, 7, 7, 7, 7, 7, 7, 11, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 28, 28, 28, 28, 28, 20, 20, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 7, 7, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 317) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184480539 none CCOC[C@H]1C(=O)N(CC)CC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 21, 10, 10, 10, 10, 10, 10, 10, 15, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 32, 32, 32, 32, 32, 21, 21, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480539 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480539 Building ZINC001184480541 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480541 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/318 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12) `ZINC001184480541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480541 none O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 29, 33, 33, 6, 6, 6, 6, 3, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 33, 33, 33, 33, 33, 10, 6, 6, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/319 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12) `ZINC001184480541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480541 none O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 37, 37, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 36, 36, 37, 37, 37, 37, 37, 14, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480541 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 Building ZINC001184480541 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480541 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 318) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12) `ZINC001184480541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480541 none O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 29, 33, 33, 6, 6, 6, 6, 3, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 33, 33, 33, 33, 33, 10, 6, 6, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 319) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12) `ZINC001184480541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480541 none O=C(CC1CC1)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C[C@@H]2CCCO[C@H]12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 37, 37, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 36, 36, 37, 37, 37, 37, 37, 14, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480541 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480541 Building ZINC001184480536 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480536 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/320 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184480536 none Nc1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 6, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/321 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184480536 none Nc1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 6, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480536 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 Building ZINC001184480536 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480536 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 320) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Nc1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184480536 none Nc1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 6, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 321) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Nc1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184480536 none Nc1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 6, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480536 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480536 Building ZINC001184480537 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480537 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/322 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184480537 none COC(=O)c1nc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 9, 30, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30, 30, 9, 3, 9, 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, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/323 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184480537 none COC(=O)c1nc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 9, 3, 9, 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, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480537 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 Building ZINC001184480537 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480537 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 322) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1nc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184480537 none COC(=O)c1nc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 9, 30, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30, 30, 9, 3, 9, 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, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 323) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1nc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184480537 none COC(=O)c1nc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 9, 3, 9, 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, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480537 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480537 Building ZINC001184480547 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480547 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/324 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480547 none O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 23, 35, 35, 35, 35, 35, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 12, 12, 35, 35, 35, 35, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/325 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480547 none O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 22, 33, 33, 33, 33, 33, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 33, 33, 33, 33, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480547 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 Building ZINC001184480547 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480547 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 324) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480547 none O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 23, 35, 35, 35, 35, 35, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 12, 12, 35, 35, 35, 35, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 325) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480547 none O=C(N1Cc2cncn2C[C@@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 22, 33, 33, 33, 33, 33, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 33, 33, 33, 33, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480547 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480547 Building ZINC001184480548 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480548 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/326 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480548 none O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 27, 36, 36, 36, 36, 36, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 14, 14, 36, 36, 36, 36, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/327 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480548 none O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 39, 39, 39, 39, 39, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 15, 15, 39, 39, 39, 39, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480548 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 Building ZINC001184480548 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480548 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 326) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480548 none O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 27, 36, 36, 36, 36, 36, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 14, 14, 36, 36, 36, 36, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 327) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480548 none O=C(N1Cc2cncn2C[C@H](COc2cccnc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 39, 39, 39, 39, 39, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 15, 15, 39, 39, 39, 39, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480548 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480548 Building ZINC001184480556 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480556 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/328 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1) `ZINC001184480556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184480556 none Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 3, 2, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/329 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1) `ZINC001184480556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184480556 none Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7] 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: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480556 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 Building ZINC001184480556 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480556 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 328) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1) `ZINC001184480556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184480556 none Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 3, 2, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 329) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1) `ZINC001184480556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184480556 none Cc1noc([C@@H]2C[C@@H]3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]3O2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7] 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: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480556 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480556 Building ZINC001184480568 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480568 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/330 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480568 none Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 15, 15, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/331 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480568 none Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 17, 17, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480568 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 Building ZINC001184480568 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480568 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 330) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480568 none Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 15, 15, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 331) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1) `ZINC001184480568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480568 none Cc1cccc(CN2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 17, 17, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480568 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480568 Building ZINC001184480837 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480837 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/332 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/333 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/334 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/334' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/335 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/335' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480837 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 Building ZINC001184480837 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480837 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 332) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 333) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 334) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 335) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480837 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 Building ZINC001184480837 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480837 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 332) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 333) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 334) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 335) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480837 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 Building ZINC001184480837 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480837 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 332) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 333) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 12, 12, 12, 12, 12, 25, 27, 27, 12, 12, 12, 11, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 16, 16, 16, 15, 15, 12, 12, 25, 25, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 334) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 335) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184480837.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184480837 none COC[C@H]1CN(CC2CC2)C[C@@]12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 12, 1, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 13, 13, 24, 24, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480837 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480837 Building ZINC001184480839 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480839 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/336 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184480839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480839 none COC(=O)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 22, 28, 22, 28, 28, 13, 6, 6, 6, 6, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 28, 28, 28, 28, 28, 28, 28, 13, 13, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/337 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184480839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480839 none COC(=O)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 30, 22, 27, 27, 14, 7, 7, 7, 7, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 27, 27, 30, 30, 30, 27, 27, 14, 14, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480839 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 Building ZINC001184480839 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480839 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 336) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184480839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480839 none COC(=O)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 22, 28, 22, 28, 28, 13, 6, 6, 6, 6, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 28, 28, 28, 28, 28, 28, 28, 13, 13, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 337) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184480839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480839 none COC(=O)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 30, 22, 27, 27, 14, 7, 7, 7, 7, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 27, 27, 30, 30, 30, 27, 27, 14, 14, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480839 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480839 Building ZINC001184480582 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480582 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/338 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480582 none O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 15, 29, 29, 29, 29, 29, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/339 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480582 none O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480582 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 Building ZINC001184480582 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480582 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 338) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480582 none O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 15, 29, 29, 29, 29, 29, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 339) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480582 none O=C(Nc1ncnc2c1ncn2[C@@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480582 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480582 Building ZINC001184480583 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480583 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/340 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480583 none O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 31, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/341 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480583 none O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 15, 28, 28, 28, 28, 28, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480583 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 Building ZINC001184480583 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480583 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 340) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480583 none O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 31, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 341) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480583 none O=C(Nc1ncnc2c1ncn2[C@H]1CCCO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 7, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 15, 28, 28, 28, 28, 28, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 8, 8, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480583 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480583 Building ZINC001184480633 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480633 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/342 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480633 none COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 18, 11, 9, 11, 11, 11, 21, 21, 21, 21, 21, 21, 9, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 9, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/343 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480633 none COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 18, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 9, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 20, 20, 20, 20, 20, 20, 20, 9, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480633 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 Building ZINC001184480633 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480633 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 342) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480633 none COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 18, 11, 9, 11, 11, 11, 21, 21, 21, 21, 21, 21, 9, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 9, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 343) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480633 none COC(=O)c1nnn(Cc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 18, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 9, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 20, 20, 20, 20, 20, 20, 20, 9, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480633 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480633 Building ZINC001184480634 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480634 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/344 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC) `ZINC001184480634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480634 none COc1cc2cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 9, 9, 9, 9, 9, 12, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 21, 18, 18, 18, 9, 9, 12, 12, 3, 5, 5, 5, 5, 9, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/345 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC) `ZINC001184480634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480634 none COc1cc2cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 9, 9, 9, 9, 9, 12, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 21, 18, 18, 18, 9, 9, 12, 12, 3, 5, 5, 5, 5, 9, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480634 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 Building ZINC001184480634 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480634 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 344) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC) `ZINC001184480634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480634 none COc1cc2cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 9, 9, 9, 9, 9, 12, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 21, 18, 18, 18, 9, 9, 12, 12, 3, 5, 5, 5, 5, 9, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 345) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC) `ZINC001184480634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480634 none COc1cc2cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)nc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 9, 9, 9, 9, 9, 12, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 21, 18, 18, 18, 9, 9, 12, 12, 3, 5, 5, 5, 5, 9, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480634 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480634 Building ZINC001184480871 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480871 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/346 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480871 none O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 13, 22, 37, 45, 45, 45, 45, 45, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 37, 37, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/347 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480871 none O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 8, 16, 24, 31, 31, 24, 31, 31, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 24, 24, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480871 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 Building ZINC001184480871 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480871 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 346) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480871 none O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 13, 22, 37, 45, 45, 45, 45, 45, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 37, 37, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 347) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480871 none O=C(N1C[C@@H]2COC[C@]2(COCc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 8, 16, 24, 31, 31, 24, 31, 31, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 24, 24, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480871 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480871 Building ZINC001184480878 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480878 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/348 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/349 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/350 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/350' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/351 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/351' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480878 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 Building ZINC001184480878 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480878 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 348) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 349) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 350) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 351) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480878 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 Building ZINC001184480878 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480878 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 348) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 349) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 350) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 351) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480878 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 Building ZINC001184480878 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480878 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 348) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 349) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 350) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 351) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480878.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184480878 none O=C(N1CCC2(CC1)CN(c1ccccn1)CCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480878 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480878 Building ZINC001184480884 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480884 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/352 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480884 none O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 27, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 16, 16, 35, 35, 35, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/353 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480884 none O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 17, 34, 39, 39, 39, 39, 39, 39, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 17, 17, 39, 39, 39, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480884 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 Building ZINC001184480884 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480884 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 352) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480884 none O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 27, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 16, 16, 35, 35, 35, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 353) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480884 none O=C(N1C[C@@H]2COC[C@]2(COc2ncccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 17, 34, 39, 39, 39, 39, 39, 39, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 17, 17, 39, 39, 39, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480884 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480884 Building ZINC001184480893 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480893 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/354 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480893 none O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 12, 12, 29, 29, 29, 29, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/355 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480893 none O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 9, 9, 32, 32, 32, 32, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480893 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 Building ZINC001184480893 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480893 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 354) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480893 none O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 12, 12, 29, 29, 29, 29, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 355) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480893 none O=C(N1CCN(Cc2c[nH]c3ncccc23)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 9, 9, 32, 32, 32, 32, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480893 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480893 Building ZINC001184480923 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480923 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/356 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480923 none CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 19, 32, 6, 19, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 35, 35, 35, 35, 35, 35, 35, 32, 32, 32, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/357 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480923 none CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 18, 31, 6, 18, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 34, 34, 34, 34, 34, 34, 34, 31, 31, 31, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480923 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 Building ZINC001184480923 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480923 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 356) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480923 none CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 19, 32, 6, 19, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 35, 35, 35, 35, 35, 35, 35, 32, 32, 32, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 357) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480923 none CC(C)N(C)C(=O)c1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 18, 31, 6, 18, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 34, 34, 34, 34, 34, 34, 34, 31, 31, 31, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480923 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480923 Building ZINC001184480935 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480935 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/358 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2c(Br)cnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184480935 none O=C(N1CCn2c(Br)cnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 17, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/359 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2c(Br)cnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184480935 none O=C(N1CCn2c(Br)cnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 17, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480935 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 Building ZINC001184480935 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480935 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 358) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2c(Br)cnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184480935 none O=C(N1CCn2c(Br)cnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 17, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 359) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2c(Br)cnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184480935 none O=C(N1CCn2c(Br)cnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 17, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480935 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480935 Building ZINC001184480947 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480947 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/360 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480947 none O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 11, 21, 21, 21, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 9, 9, 21, 21, 21, 21, 21, 21, 21, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/361 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480947 none O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 21, 23, 23, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 12, 12, 21, 21, 23, 23, 23, 23, 23, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480947 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 Building ZINC001184480947 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480947 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 360) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480947 none O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 11, 21, 21, 21, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 9, 9, 21, 21, 21, 21, 21, 21, 21, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 361) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480947 none O=C(N1Cc2cncn2C[C@@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 21, 23, 23, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 12, 12, 21, 21, 23, 23, 23, 23, 23, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480947 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480947 Building ZINC001184480948 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480948 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/362 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480948 none O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 13, 27, 31, 31, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 31, 31, 31, 31, 31, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/363 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480948 none O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 14, 27, 29, 29, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 9, 9, 27, 27, 29, 29, 29, 29, 29, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480948 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 Building ZINC001184480948 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480948 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 362) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480948 none O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 13, 27, 31, 31, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 31, 31, 31, 31, 31, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 363) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184480948 none O=C(N1Cc2cncn2C[C@H](COCC2CC2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 14, 27, 29, 29, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 9, 9, 27, 27, 29, 29, 29, 29, 29, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480948 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480948 Building ZINC001184480950 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480950 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/364 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480950 none O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 6, 6, 6, 6, 24, 40, 40, 40, 40, 40, 6, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/365 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480950 none O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 20, 31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480950 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 Building ZINC001184480950 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480950 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 364) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480950 none O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 6, 6, 6, 6, 24, 40, 40, 40, 40, 40, 6, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 365) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480950 none O=C(N1CC[C@]2(C[C@@H](Oc3cccnc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 20, 31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 19, 20, 21] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480950 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480950 Building ZINC001184480977 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480977 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/366 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/367 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/368 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/368' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/369 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/369' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480977 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 Building ZINC001184480977 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480977 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 366) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 367) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 368) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 369) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480977 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 Building ZINC001184480977 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480977 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 366) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 367) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 368) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 369) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480977 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 Building ZINC001184480977 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480977 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 366) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 367) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 368) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 369) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480977 none O=C(N[C@H]1CC[N@@](c2ccc(Cl)nn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 8, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480977 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480977 Building ZINC001184480994 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480994 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/370 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480994 none O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 15, 15, 19, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 19, 19, 57, 66, 22, 22, 22, 22, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 246 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/371 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480994 none O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 14, 14, 19, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 57, 60, 20, 20, 20, 20, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 232 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480994 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 Building ZINC001184480994 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480994 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 370) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480994 none O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 15, 15, 19, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 19, 19, 57, 66, 22, 22, 22, 22, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 246 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 371) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480994 none O=C(N[C@@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 14, 14, 19, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 57, 60, 20, 20, 20, 20, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 232 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184480994 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184480994 Building ZINC001184481000 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481000 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/372 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481000 none O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 16, 16, 19, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 57, 57, 19, 19, 19, 19, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/373 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481000 none O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 13, 13, 20, 13, 25, 25, 25, 26, 26, 25, 25, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 60, 75, 26, 26, 26, 26, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 285 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481000 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 Building ZINC001184481000 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481000 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 372) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481000 none O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 16, 16, 19, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 57, 57, 19, 19, 19, 19, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 373) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481000 none O=C(N[C@H](CO)[C@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 13, 13, 20, 13, 25, 25, 25, 26, 26, 25, 25, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 60, 75, 26, 26, 26, 26, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 285 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481000 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481000 Building ZINC001184481001 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481001 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/374 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481001 none O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 13, 13, 20, 13, 25, 25, 25, 26, 26, 25, 25, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 60, 75, 26, 26, 26, 26, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 285 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/375 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481001 none O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 17, 17, 20, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 20, 20, 60, 60, 20, 20, 20, 20, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 223 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481001 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 Building ZINC001184481001 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481001 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 374) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481001 none O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 13, 13, 20, 13, 25, 25, 25, 26, 26, 25, 25, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 60, 75, 26, 26, 26, 26, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 285 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 375) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481001 none O=C(N[C@@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 17, 17, 20, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 20, 20, 60, 60, 20, 20, 20, 20, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 223 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481001 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481001 Building ZINC001184481003 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481003 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/376 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481003 none O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 14, 14, 19, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 57, 57, 19, 19, 19, 19, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/377 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481003 none O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 15, 15, 19, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 19, 19, 57, 66, 22, 22, 22, 22, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 246 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481003 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 Building ZINC001184481003 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481003 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 376) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481003 none O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 14, 14, 19, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 57, 57, 19, 19, 19, 19, 8, 8, 8, 8] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 377) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481003 none O=C(N[C@H](CO)[C@@H](O)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 15, 15, 19, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 19, 19, 57, 66, 22, 22, 22, 22, 7, 7, 7, 7] 450 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 246 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481003 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481003 Building ZINC001184481108 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481108 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/378 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ncnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481108 none CC(C)Oc1ncnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/379 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ncnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481108 none CC(C)Oc1ncnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481108 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 Building ZINC001184481108 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481108 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 378) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)Oc1ncnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481108 none CC(C)Oc1ncnc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 379) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)Oc1ncnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481108 none CC(C)Oc1ncnc2c1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481108 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481108 Building ZINC001184481131 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481131 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/380 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1) `ZINC001184481131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481131 none CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 31, 31, 20, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 34, 34, 34, 34, 34, 34, 34, 31, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/381 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1) `ZINC001184481131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481131 none CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 32, 27, 27, 19, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 32, 32, 32, 32, 32, 32, 32, 27, 19, 19, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481131 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 Building ZINC001184481131 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481131 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 380) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1) `ZINC001184481131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481131 none CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 31, 31, 20, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 34, 34, 34, 34, 34, 34, 34, 31, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 381) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1) `ZINC001184481131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481131 none CC(C)C(=O)NC[C@@H]1CCC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 32, 27, 27, 19, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 32, 32, 32, 32, 32, 32, 32, 27, 19, 19, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481131 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481131 Building ZINC001184481136 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481136 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/382 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 37, 11, 37, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/383 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 11, 36, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/384 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/384' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 11, 34, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 35, 35, 35, 35, 35, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/385 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/385' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 10, 34, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 10, 10, 35, 35, 35, 35, 35, 10, 10, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481136 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 Building ZINC001184481136 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481136 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 382) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 37, 11, 37, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 383) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 11, 36, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 384) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 11, 34, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 35, 35, 35, 35, 35, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 385) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 10, 34, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 10, 10, 35, 35, 35, 35, 35, 10, 10, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481136 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 Building ZINC001184481136 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481136 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 382) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 37, 11, 37, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 383) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 11, 36, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 384) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 11, 34, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 35, 35, 35, 35, 35, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 385) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 10, 34, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 10, 10, 35, 35, 35, 35, 35, 10, 10, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481136 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 Building ZINC001184481136 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481136 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 382) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 37, 11, 37, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 383) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 11, 36, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 38, 38, 38, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 384) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 11, 34, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 35, 35, 35, 35, 35, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 385) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1) `ZINC001184481136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481136 none CCOC(=O)[C@H]1CC[N@@](C2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 10, 34, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 10, 10, 35, 35, 35, 35, 35, 10, 10, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 46, 44, 16, 17, 29, 51, 52, 14, 54, 18, 15, 42, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481136 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481136 Building ZINC001184481170 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481170 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/386 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1) `ZINC001184481170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481170 none Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 10, 22, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 10, 10, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/387 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1) `ZINC001184481170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481170 none Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 12, 22, 31, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 12, 12, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481170 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 Building ZINC001184481170 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481170 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 386) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1) `ZINC001184481170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481170 none Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 10, 22, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 10, 10, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 387) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1) `ZINC001184481170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481170 none Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 12, 22, 31, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 12, 12, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481170 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481170 Building ZINC001184481174 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481174 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/388 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1) `ZINC001184481174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481174 none Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 13, 22, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 4, 4, 13, 13, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/389 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1) `ZINC001184481174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481174 none Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 10, 21, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 10, 10, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481174 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 Building ZINC001184481174 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481174 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 388) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1) `ZINC001184481174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481174 none Cn1ncc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 13, 22, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 4, 4, 13, 13, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 389) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1) `ZINC001184481174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481174 none Cn1ncc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C[C@@H]2COc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 10, 21, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 10, 10, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481174 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481174 Building ZINC001184481178 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481178 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/390 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481178 none Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 8, 7, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 33, 33, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 33] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/391 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481178 none Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7, 24] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481178 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 Building ZINC001184481178 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481178 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 390) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481178 none Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 8, 7, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 33, 33, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 33] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 391) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481178 none Cn1cc([C@@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7, 24] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481178 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481178 Building ZINC001184481182 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481182 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/392 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481182 none Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12, 32] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/393 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481182 none Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481182 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 Building ZINC001184481182 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481182 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 392) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481182 none Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12, 32] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 393) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1) `ZINC001184481182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481182 none Cn1cc([C@H]2COC3(C2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481182 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481182 Building ZINC001184481238 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481238 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/394 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCOc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481238 none O=C(N1CCN(CCOc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 11, 15, 33, 33, 33, 33, 33, 33, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 11, 11, 15, 15, 33, 33, 33, 33, 33, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/395 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCOc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481238 none O=C(N1CCN(CCOc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 10, 14, 34, 34, 34, 34, 34, 34, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 10, 10, 14, 14, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481238 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 Building ZINC001184481238 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481238 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 394) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCOc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481238 none O=C(N1CCN(CCOc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 11, 15, 33, 33, 33, 33, 33, 33, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 11, 11, 15, 15, 33, 33, 33, 33, 33, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 395) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCOc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481238 none O=C(N1CCN(CCOc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 10, 14, 34, 34, 34, 34, 34, 34, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 10, 10, 14, 14, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481238 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481238 Building ZINC001184481247 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481247 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/396 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184481247 none O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 5, 10, 5, 5, 7, 5, 5, 5, 12, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/397 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184481247 none O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 5, 10, 5, 5, 7, 5, 5, 5, 12, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 8, 16, 16, 16, 16, 16, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481247 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 Building ZINC001184481247 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481247 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 396) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184481247 none O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 5, 10, 5, 5, 7, 5, 5, 5, 12, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 397) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184481247 none O=C(N(c1ccccn1)[C@@H]1CNC[C@@H]2CCCO[C@H]12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 5, 10, 5, 5, 7, 5, 5, 5, 12, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 8, 16, 16, 16, 16, 16, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481247 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481247 Building ZINC001184481248 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481248 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/398 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2) `ZINC001184481248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481248 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 13, 20, 20, 20, 17, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 71 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/399 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2) `ZINC001184481248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481248 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 13, 19, 19, 19, 16, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481248 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 Building ZINC001184481248 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481248 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 398) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2) `ZINC001184481248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481248 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 13, 20, 20, 20, 17, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 71 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 399) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2) `ZINC001184481248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184481248 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ncnc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 13, 19, 19, 19, 16, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481248 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481248 Building ZINC001184481265 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481265 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/400 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481265 none O=C(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 18, 34, 34, 34, 34, 34, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 18, 34, 34, 34, 34, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/401 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481265 none O=C(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 13, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 12, 12, 13, 23, 23, 23, 23, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481265 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 Building ZINC001184481265 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481265 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 400) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481265 none O=C(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 18, 34, 34, 34, 34, 34, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 18, 34, 34, 34, 34, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 401) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481265 none O=C(N1CCCn2nnc(CNc3cccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 13, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 12, 12, 13, 23, 23, 23, 23, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481265 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481265 Building ZINC001184481295 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481295 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/402 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481295 none O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 18, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 6, 4, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 17, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/403 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481295 none O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 36, 36, 36, 11, 11, 11, 11, 11, 11, 11, 9, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 19, 36, 36, 36, 36, 36, 36, 36, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481295 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 Building ZINC001184481295 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481295 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 402) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481295 none O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 18, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 6, 4, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 17, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 403) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481295 none O=C(NC1CCC1)[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 36, 36, 36, 11, 11, 11, 11, 11, 11, 11, 9, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 19, 36, 36, 36, 36, 36, 36, 36, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481295 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481295 Building ZINC001184481300 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481300 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/404 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481300 none O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 19, 19, 32, 32, 32, 7, 7, 7, 7, 7, 7, 7, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 19, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/405 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481300 none O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 21, 21, 36, 36, 36, 8, 8, 8, 8, 8, 8, 8, 6, 5, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 21, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481300 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 Building ZINC001184481300 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481300 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 404) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481300 none O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 19, 19, 32, 32, 32, 7, 7, 7, 7, 7, 7, 7, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 19, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 405) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481300 none O=C(NC1CCC1)[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 21, 21, 36, 36, 36, 8, 8, 8, 8, 8, 8, 8, 6, 5, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 21, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481300 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481300 Building ZINC001184481318 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481318 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/406 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481318 none O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 57, 19, 19, 19, 19, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/407 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481318 none O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 48, 16, 16, 16, 16, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481318 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 Building ZINC001184481318 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481318 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 406) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481318 none O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 57, 19, 19, 19, 19, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 407) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481318 none O=C(N1CC[C@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 48, 16, 16, 16, 16, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481318 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481318 Building ZINC001184481323 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481323 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/408 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481323 none O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 54, 18, 18, 18, 18, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/409 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481323 none O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481323 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 Building ZINC001184481323 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481323 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 408) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481323 none O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 54, 18, 18, 18, 18, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 409) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481323 none O=C(N1CC[C@@H](F)[C@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481323 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481323 Building ZINC001184481326 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481326 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/410 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481326 none O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/411 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481326 none O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 60, 20, 20, 20, 20, 5, 5, 5, 5] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481326 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 Building ZINC001184481326 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481326 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 410) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481326 none O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 411) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481326 none O=C(N1CC[C@@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 60, 20, 20, 20, 20, 5, 5, 5, 5] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/236261/xbz-8058088.52/working/building/ZINC001184481326 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481326 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481326 Building ZINC001184481329 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481329 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/412 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481329 none O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/413 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481329 none O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481329 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 Building ZINC001184481329 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481329 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 412) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481329 none O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 413) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184481329 none O=C(N1CC[C@H](F)[C@@](O)(C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 15, 5, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 57, 19, 19, 19, 19, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/236261/xbz-8058088.52/working/building/ZINC001184481329 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481329 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481329 Building ZINC001184481301 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481301 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/414 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COCCN2CCCC2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481301 none O=C(N1CCC(COCCN2CCCC2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 10, 17, 27, 27, 36, 36, 36, 36, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/415 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COCCN2CCCC2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481301 none O=C(N1CCC(COCCN2CCCC2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 11, 17, 27, 27, 38, 38, 38, 38, 3, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 11, 11, 27, 27, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481301 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 Building ZINC001184481301 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481301 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC(COCCN2CCCC2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481301 none O=C(N1CCC(COCCN2CCCC2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 10, 17, 27, 27, 36, 36, 36, 36, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC(COCCN2CCCC2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184481301 none O=C(N1CCC(COCCN2CCCC2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 11, 17, 27, 27, 38, 38, 38, 38, 3, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 11, 11, 27, 27, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481301 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481301 Building ZINC001184481421 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481421 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/416 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1) `ZINC001184481421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481421 none O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 18, 22, 35, 35, 35, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/417 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1) `ZINC001184481421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481421 none O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 37, 37, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 18, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 112 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481421 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 Building ZINC001184481421 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481421 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 416) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1) `ZINC001184481421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481421 none O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 18, 22, 35, 35, 35, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 417) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1) `ZINC001184481421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184481421 none O=C(NC1CCC1)[C@H]1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 37, 37, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 18, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 112 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481421 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481421 Building ZINC001184481427 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481427 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/418 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481427 none O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 16, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 29, 29, 29, 6, 6, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/419 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481427 none O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 17, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 34, 34, 34, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481427 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 Building ZINC001184481427 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481427 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 418) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481427 none O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 16, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 29, 29, 29, 6, 6, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 419) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184481427 none O=C(N1CCO[C@H]2[C@@H](Oc3ncccc3F)CC[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 7, 12, 1, 8, 1, 1, 1, 1, 15, 5, 5, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 17, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 34, 34, 34, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481427 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481427 Building ZINC001184481549 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481549 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/420 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481549 none O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 17, 17, 17, 28, 31, 34, 38, 38, 38, 38, 38, 17, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 17, 17, 17, 31, 31, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/421 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481549 none O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 17, 17, 17, 26, 29, 32, 35, 35, 35, 35, 35, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 17, 17, 17, 29, 29, 32, 32, 35, 35, 35, 35, 35, 35, 35, 35, 17, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481549 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 Building ZINC001184481549 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481549 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 420) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481549 none O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 17, 17, 17, 28, 31, 34, 38, 38, 38, 38, 38, 17, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 17, 17, 17, 31, 31, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 421) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481549 none O=C(NCc1cccc(OCCN2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 17, 17, 17, 26, 29, 32, 35, 35, 35, 35, 35, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 17, 17, 17, 29, 29, 32, 32, 35, 35, 35, 35, 35, 35, 35, 35, 17, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184481549 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184481549 Building ZINC001184484229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/422 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/423 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/424 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/424' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/425 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/425' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 Building ZINC001184484229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 Building ZINC001184484229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 Building ZINC001184484229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 25, 25, 25, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 26, 26, 25, 25, 25, 25, 8, 8, 8, 8, 3, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484229.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184484229 none NC(=O)[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 11, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 23, 23, 23, 23, 8, 8, 8, 8, 3, 6, 6, 6, 6, 23, 23, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484229 Building ZINC001184484271 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484271 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/426 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/427 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/428 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/428' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/429 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/429' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484271 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 Building ZINC001184484271 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484271 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 426) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 427) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 428) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 429) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484271 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 Building ZINC001184484271 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484271 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 426) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 427) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 428) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 429) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484271 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 Building ZINC001184484271 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484271 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 426) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 427) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 21, 21, 17, 21, 21, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 21, 21, 17, 21, 21, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 428) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 429) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484271 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 16, 18, 18, 16, 18, 18, 7, 14, 14, 14, 3, 4, 4, 4, 4, 7, 7, 7, 7, 16, 16, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484271 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484271 Building ZINC001184484272 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484272 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/430 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/431 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/432 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/432' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/433 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/433' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484272 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 Building ZINC001184484272 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484272 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 430) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 431) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 432) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 433) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484272 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 Building ZINC001184484272 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484272 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 430) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 431) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 432) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 433) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484272 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 Building ZINC001184484272 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484272 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 430) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 431) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 22, 25, 25, 22, 25, 25, 10, 15, 15, 15, 3, 4, 4, 4, 4, 10, 10, 10, 10, 22, 22, 25, 25, 22, 25, 25, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 432) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 433) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1) `ZINC001184484272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184484272 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 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, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 19, 23, 23, 19, 23, 23, 8, 16, 16, 16, 3, 4, 4, 4, 4, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484272 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484272 Building ZINC001184484321 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484321 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/434 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21) `ZINC001184484321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484321 none CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 26, 18, 26, 18, 18, 18, 18, 18, 18, 6, 18, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 3, 6, 6, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/435 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21) `ZINC001184484321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484321 none CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 18, 21, 18, 18, 18, 18, 18, 18, 7, 18, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 18, 18, 4, 7, 7, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484321 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 Building ZINC001184484321 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484321 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 434) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21) `ZINC001184484321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484321 none CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 26, 18, 26, 18, 18, 18, 18, 18, 18, 6, 18, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 3, 6, 6, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 435) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21) `ZINC001184484321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484321 none CC(C)(C)OC(=O)N1CCO[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 18, 21, 18, 18, 18, 18, 18, 18, 7, 18, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 18, 18, 4, 7, 7, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484321 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484321 Building ZINC001184484424 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484424 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/436 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1) `ZINC001184484424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484424 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 12, 1, 5, 11, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 13, 6, 6, 14, 21, 21, 6, 8, 8, 8, 6, 3, 5, 5, 5, 5, 13, 13, 13, 21, 21, 21, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/437 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1) `ZINC001184484424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484424 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 12, 1, 5, 11, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 13, 6, 6, 14, 21, 21, 6, 8, 8, 8, 6, 3, 4, 4, 4, 4, 13, 13, 13, 21, 21, 21, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484424 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 Building ZINC001184484424 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484424 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 436) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1) `ZINC001184484424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484424 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 12, 1, 5, 11, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 13, 6, 6, 14, 21, 21, 6, 8, 8, 8, 6, 3, 5, 5, 5, 5, 13, 13, 13, 21, 21, 21, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 437) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1) `ZINC001184484424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484424 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(OC)c(OC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 12, 1, 5, 11, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 13, 6, 6, 14, 21, 21, 6, 8, 8, 8, 6, 3, 4, 4, 4, 4, 13, 13, 13, 21, 21, 21, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484424 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484424 Building ZINC001184484398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/438 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 15, 15, 30, 30, 30, 30, 30, 15, 15, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/439 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 32, 32, 32, 32, 32, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/440 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/440' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 16, 16, 23, 23, 23, 23, 23, 16, 16, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/441 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/441' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 39, 39, 39, 39, 39, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 Building ZINC001184484398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 438) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 15, 15, 30, 30, 30, 30, 30, 15, 15, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 439) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 32, 32, 32, 32, 32, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 440) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 16, 16, 23, 23, 23, 23, 23, 16, 16, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 441) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 39, 39, 39, 39, 39, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 Building ZINC001184484398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 438) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 15, 15, 30, 30, 30, 30, 30, 15, 15, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 439) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 32, 32, 32, 32, 32, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 440) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 16, 16, 23, 23, 23, 23, 23, 16, 16, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 441) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 39, 39, 39, 39, 39, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 Building ZINC001184484398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 438) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 15, 15, 30, 30, 30, 30, 30, 15, 15, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 439) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 32, 32, 32, 32, 32, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 440) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 16, 16, 23, 23, 23, 23, 23, 16, 16, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 441) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484398 none O=C(N[C@H]1C[N@@](c2ncnc3ccccc32)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 39, 39, 39, 39, 39, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484398 Building ZINC001184484426 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484426 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/442 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC(=S)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N) `ZINC001184484426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184484426 none COC(=O)NC(=S)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 6, 4, 7, 3, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 13, 7, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 15, 15, 15, 15, 31, 31, 31, 20, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/443 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC(=S)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N) `ZINC001184484426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184484426 none COC(=O)NC(=S)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 6, 4, 7, 3, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 30, 13, 7, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 11, 15, 15, 15, 30, 30, 30, 20, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484426 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 Building ZINC001184484426 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484426 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 442) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)NC(=S)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N) `ZINC001184484426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184484426 none COC(=O)NC(=S)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 6, 4, 7, 3, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 13, 7, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 15, 15, 15, 15, 31, 31, 31, 20, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 443) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)NC(=S)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N) `ZINC001184484426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184484426 none COC(=O)NC(=S)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1ccccc1N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 14, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 6, 4, 7, 3, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 30, 13, 7, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 15, 15, 11, 15, 15, 15, 30, 30, 30, 20, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484426 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484426 Building ZINC001184484432 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484432 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/444 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484432 none COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 21, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 21, 21, 21, 21, 21, 21, 14, 14, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/445 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484432 none COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 30, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 30, 30, 30, 30, 30, 30, 20, 20, 4, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484432 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 Building ZINC001184484432 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484432 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 444) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484432 none COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 21, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 21, 21, 21, 21, 21, 21, 14, 14, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 445) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484432 none COc1ccc2c(c1)NC(=O)C[C@@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 30, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 30, 30, 30, 30, 30, 30, 20, 20, 4, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484432 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484432 Building ZINC001184484433 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484433 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/446 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484433 none COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 30, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 30, 30, 30, 30, 30, 30, 20, 20, 4, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/447 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484433 none COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 22, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 22, 22, 22, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484433 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 Building ZINC001184484433 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484433 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 446) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484433 none COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 30, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 30, 30, 30, 30, 30, 30, 20, 20, 4, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 447) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484433 none COc1ccc2c(c1)NC(=O)C[C@H]2CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 22, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 22, 22, 22, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484433 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484433 Building ZINC001184484463 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484463 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/448 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nn(C)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12) `ZINC001184484463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184484463 none COC(=O)c1nn(C)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 15, 26, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 26, 26, 26, 15, 15, 15, 15, 15, 3, 4, 4, 4, 4, 15] 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/449 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1nn(C)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12) `ZINC001184484463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184484463 none COC(=O)c1nn(C)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 25, 25, 25, 15, 15, 15, 15, 15, 3, 4, 4, 4, 4, 15] 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484463 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 Building ZINC001184484463 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484463 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 448) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1nn(C)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12) `ZINC001184484463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184484463 none COC(=O)c1nn(C)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 15, 26, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 26, 26, 26, 15, 15, 15, 15, 15, 3, 4, 4, 4, 4, 15] 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 449) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1nn(C)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12) `ZINC001184484463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184484463 none COC(=O)c1nn(C)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 25, 25, 25, 15, 15, 15, 15, 15, 3, 4, 4, 4, 4, 15] 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484463 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484463 Building ZINC001184484607 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484607 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/450 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484607 none COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 11, 3, 5, 5, 9, 10, 11, 21, 28, 28, 28, 28, 28, 28, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 10, 10, 10, 10, 11, 11, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/451 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484607 none COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 2, 5, 5, 8, 10, 15, 28, 38, 38, 38, 38, 38, 38, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 15, 15, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484607 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 Building ZINC001184484607 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484607 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 450) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484607 none COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 11, 3, 5, 5, 9, 10, 11, 21, 28, 28, 28, 28, 28, 28, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 10, 10, 10, 10, 11, 11, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 451) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484607 none COC(=O)[C@H](CCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 2, 5, 5, 8, 10, 15, 28, 38, 38, 38, 38, 38, 38, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 15, 15, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484607 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484607 Building ZINC001184484638 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484638 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/452 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184484638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184484638 none CC(C)CC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 12, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 48 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/453 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184484638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184484638 none CC(C)CC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 13, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484638 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 Building ZINC001184484638 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484638 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 452) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)CC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184484638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184484638 none CC(C)CC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 12, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 48 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 453) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)CC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184484638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184484638 none CC(C)CC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 13, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484638 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484638 Building ZINC001184484885 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484885 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/454 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184484885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484885 none CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 33, 26, 33, 26, 26, 26, 26, 26, 26, 26, 23, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 26, 26, 26, 26, 16, 16, 3, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/455 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184484885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484885 none CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 27, 37, 27, 27, 27, 27, 27, 27, 27, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 27, 27, 27, 27, 27, 14, 14, 3, 4, 4, 4, 4, 27, 27] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484885 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 Building ZINC001184484885 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484885 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 454) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184484885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484885 none CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 33, 26, 33, 26, 26, 26, 26, 26, 26, 26, 23, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 26, 26, 26, 26, 16, 16, 3, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 455) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184484885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184484885 none CC(C)(C)OC(=O)N1C[C@H]2COC[C@@]2(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 27, 37, 27, 27, 27, 27, 27, 27, 27, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 27, 27, 27, 27, 27, 14, 14, 3, 4, 4, 4, 4, 27, 27] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484885 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484885 Building ZINC001184484919 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484919 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/456 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1) `ZINC001184484919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484919 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 32, 44, 44, 44, 24, 24, 24, 17, 6, 6, 2, 3, 3, 3, 3, 17, 17, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/457 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1) `ZINC001184484919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484919 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 37, 44, 44, 44, 21, 21, 21, 14, 7, 7, 2, 3, 3, 3, 3, 14, 14, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484919 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 Building ZINC001184484919 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484919 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 456) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1) `ZINC001184484919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484919 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 32, 44, 44, 44, 24, 24, 24, 17, 6, 6, 2, 3, 3, 3, 3, 17, 17, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 457) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1) `ZINC001184484919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484919 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1OC1COC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 37, 44, 44, 44, 21, 21, 21, 14, 7, 7, 2, 3, 3, 3, 3, 14, 14, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484919 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484919 Building ZINC001184484928 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484928 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/458 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 14, 36, 14, 14, 14, 12, 8, 13, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 14, 36, 36, 36, 14, 14, 13, 13, 3, 5, 5, 5, 5, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/459 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 6, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 28, 28, 28, 10, 10, 10, 10, 3, 4, 4, 4, 4, 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, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/460 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/460' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 14, 37, 14, 14, 14, 3, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 37, 37, 37, 14, 14, 12, 12, 3, 4, 4, 4, 4, 12, 12, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/461 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/461' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 12, 30, 12, 12, 12, 11, 6, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 12, 30, 30, 30, 12, 12, 11, 11, 3, 4, 4, 4, 4, 11, 11, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484928 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 Building ZINC001184484928 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484928 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 458) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 14, 36, 14, 14, 14, 12, 8, 13, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 14, 36, 36, 36, 14, 14, 13, 13, 3, 5, 5, 5, 5, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 459) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 6, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 28, 28, 28, 10, 10, 10, 10, 3, 4, 4, 4, 4, 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, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 460) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 14, 37, 14, 14, 14, 3, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 37, 37, 37, 14, 14, 12, 12, 3, 4, 4, 4, 4, 12, 12, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 461) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 12, 30, 12, 12, 12, 11, 6, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 12, 30, 30, 30, 12, 12, 11, 11, 3, 4, 4, 4, 4, 11, 11, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484928 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 Building ZINC001184484928 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484928 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 458) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 14, 36, 14, 14, 14, 12, 8, 13, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 14, 36, 36, 36, 14, 14, 13, 13, 3, 5, 5, 5, 5, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 459) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 6, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 28, 28, 28, 10, 10, 10, 10, 3, 4, 4, 4, 4, 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, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 460) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 14, 37, 14, 14, 14, 3, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 37, 37, 37, 14, 14, 12, 12, 3, 4, 4, 4, 4, 12, 12, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 461) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 12, 30, 12, 12, 12, 11, 6, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 12, 30, 30, 30, 12, 12, 11, 11, 3, 4, 4, 4, 4, 11, 11, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484928 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 Building ZINC001184484928 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484928 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 458) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 14, 36, 14, 14, 14, 12, 8, 13, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 14, 36, 36, 36, 14, 14, 13, 13, 3, 5, 5, 5, 5, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 459) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 10, 28, 10, 10, 10, 6, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 28, 28, 28, 10, 10, 10, 10, 3, 4, 4, 4, 4, 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, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 460) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 14, 37, 14, 14, 14, 3, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 37, 37, 37, 14, 14, 12, 12, 3, 4, 4, 4, 4, 12, 12, 14, 14] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 461) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1) `ZINC001184484928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484928 none COC(=O)[C@H]1C[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 12, 30, 12, 12, 12, 11, 6, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 12, 30, 30, 30, 12, 12, 11, 11, 3, 4, 4, 4, 4, 11, 11, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484928 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484928 Building ZINC001184484984 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484984 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/462 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184484984 none C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 22, 22, 23, 23, 23, 23, 23, 10, 10, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/463 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184484984 none C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 10, 10, 19, 19, 21, 21, 19, 21, 21, 10, 10, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484984 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 Building ZINC001184484984 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484984 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 462) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184484984 none C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 22, 22, 23, 23, 23, 23, 23, 10, 10, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 463) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184484984 none C[C@@H]1CN(C(=O)c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 10, 10, 19, 19, 21, 21, 19, 21, 21, 10, 10, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184484984 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184484984 Building ZINC001184485029 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485029 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/464 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485029 none O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 17, 17, 14, 23, 36, 36, 36, 36, 36, 36, 36, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/465 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485029 none O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 16, 16, 14, 22, 34, 34, 34, 34, 34, 34, 34, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485029 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 Building ZINC001184485029 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485029 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 464) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485029 none O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 17, 17, 14, 23, 36, 36, 36, 36, 36, 36, 36, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 465) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485029 none O=C(NCc1ccc(N2CCCCS2(=O)=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 16, 16, 14, 22, 34, 34, 34, 34, 34, 34, 34, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485029 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485029 Building ZINC001184485021 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485021 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/466 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/467 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/468 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/468' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/469 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/469' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485021 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 Building ZINC001184485021 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485021 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 466) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 467) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 468) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 469) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485021 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 Building ZINC001184485021 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485021 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 466) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 467) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 468) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 469) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485021 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 Building ZINC001184485021 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485021 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 466) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 467) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 18, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 468) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 469) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485021.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485021 none COC(=O)C[C@@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 3, 3, 3, 3, 3, 3, 7, 12, 12, 7, 12, 12, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 7, 7, 3, 3, 7, 7, 12, 12, 7, 12, 12, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485021 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485021 Building ZINC001184485023 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485023 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/470 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/471 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/472 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/472' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/473 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/473' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485023 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 Building ZINC001184485023 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485023 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 470) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 471) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 472) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 473) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485023 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 Building ZINC001184485023 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485023 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 470) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 471) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 472) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 473) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485023 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 Building ZINC001184485023 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485023 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 470) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 471) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 20, 2, 2, 2, 2, 2, 2, 8, 13, 13, 8, 13, 13, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 6, 6, 2, 2, 8, 8, 13, 13, 8, 13, 13, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 472) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 473) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485023.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184485023 none COC(=O)C[C@H]1CN(Cc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 4, 16, 2, 2, 2, 2, 2, 2, 4, 8, 8, 4, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 4, 4, 2, 2, 4, 4, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485023 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485023 Building ZINC001184485080 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485080 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/474 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485080 none O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 8, 8, 8, 6, 8, 12, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 20, 20, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/475 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485080 none O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 8, 8, 8, 6, 8, 12, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 20, 20, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485080 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 Building ZINC001184485080 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485080 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 474) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485080 none O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 8, 8, 8, 6, 8, 12, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 20, 20, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 475) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485080 none O=C(Nc1cccc2c(=O)cc(c3nn[nH]n3)oc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'O.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 8, 8, 8, 6, 8, 12, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 20, 20, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485080 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485080 Building ZINC001184485146 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485146 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/476 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485146 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/477 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485146 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 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]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485146 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 Building ZINC001184485146 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485146 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 476) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485146 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 477) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485146 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 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]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485146 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485146 Building ZINC001184485149 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485149 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/478 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485149 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 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]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/479 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485149 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485149 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 Building ZINC001184485149 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485149 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 478) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485149 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 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]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 479) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21) `ZINC001184485149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485149 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)Cc2nnc(C(F)(F)F)n21 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', '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, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 8, 8, 1, 5, 15, 15, 15, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485149 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485149 Building ZINC001184485203 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485203 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/480 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/481 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/482 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/482' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/483 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/483' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485203 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 Building ZINC001184485203 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485203 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 480) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 481) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 482) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 483) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485203 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 Building ZINC001184485203 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485203 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 480) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 481) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 482) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 483) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485203 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 Building ZINC001184485203 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485203 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 480) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 481) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 482) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 483) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485203.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485203 none O=C(N1CCC2(CC1)C(=O)NCN2c1ccc(F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 12, 12, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485203 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485203 Building ZINC001184485207 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485207 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/484 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(C(=O)c2ccccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184485207 none O=C(N[C@H]1CCN(C(=O)c2ccccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 18, 18, 28, 28, 28, 28, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/485 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(C(=O)c2ccccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184485207 none O=C(N[C@H]1CCN(C(=O)c2ccccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 22, 22, 32, 32, 32, 32, 32, 32, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 32, 32, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485207 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 Building ZINC001184485207 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485207 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 484) grep: /scratch/xiaobo/236261/xbz-8058088.52/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]1CCN(C(=O)c2ccccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184485207 none O=C(N[C@H]1CCN(C(=O)c2ccccc2F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 18, 18, 28, 28, 28, 28, 28, 28, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 485) grep: /scratch/xiaobo/236261/xbz-8058088.52/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]1CCN(C(=O)c2ccccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184485207 none O=C(N[C@H]1CCN(C(=O)c2ccccc2F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 16, 16, 22, 22, 32, 32, 32, 32, 32, 32, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 32, 32, 32, 32, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485207 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485207 Building ZINC001184485248 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485248 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/486 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O) `ZINC001184485248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485248 none Cn1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 6, 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]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/487 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O) `ZINC001184485248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485248 none Cn1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 6, 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]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485248 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 Building ZINC001184485248 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485248 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 486) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O) `ZINC001184485248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485248 none Cn1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 6, 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]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 487) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O) `ZINC001184485248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485248 none Cn1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 6, 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]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485248 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485248 Building ZINC001184485278 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485278 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/488 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485278 none O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 9, 9, 31, 31, 31, 31, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/489 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485278 none O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 10, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 32, 32, 32, 32, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485278 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 Building ZINC001184485278 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485278 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 488) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485278 none O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 9, 9, 31, 31, 31, 31, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 489) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485278 none O=C(NC[C@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 10, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 32, 32, 32, 32, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485278 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485278 Building ZINC001184485279 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485279 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/490 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485279 none O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 10, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 32, 32, 32, 32, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/491 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485279 none O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 9, 9, 31, 31, 31, 31, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485279 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 Building ZINC001184485279 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485279 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 490) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485279 none O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 10, 10, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 10, 10, 32, 32, 32, 32, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 491) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184485279 none O=C(NC[C@@H]1Cn2nnc(c3cccc(F)c3)c2CO1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 9, 9, 31, 31, 31, 31, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485279 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485279 Building ZINC001184485290 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485290 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/492 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/493 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/494 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/494' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/495 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/495' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485290 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 Building ZINC001184485290 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485290 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 492) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 493) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 494) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 495) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485290 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 Building ZINC001184485290 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485290 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 492) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 493) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 494) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 495) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485290 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 Building ZINC001184485290 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485290 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 492) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 493) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 13, 25, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 494) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1) `ZINC001184485290.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 495) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1) `ZINC001184485290.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485290 none CC(C)(C)OC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC[C@H](N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 13, 24, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485290 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485290 Building ZINC001184485525 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485525 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/496 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1) `ZINC001184485525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485525 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/497 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1) `ZINC001184485525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485525 none COc1cc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485525 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 Building ZINC001184485525 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485525 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 496) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1) `ZINC001184485525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485525 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 497) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1) `ZINC001184485525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485525 none COc1cc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485525 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485525 Building ZINC001184485533 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485533 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/498 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184485533 none COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 7, 7, 7, 7, 8, 25, 25, 25, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 7, 2, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/499 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184485533 none COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 7, 7, 7, 7, 8, 24, 24, 24, 24, 24, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 7, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485533 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 Building ZINC001184485533 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485533 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 498) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184485533 none COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 7, 7, 7, 7, 8, 25, 25, 25, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 7, 2, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 499) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184485533 none COC(=O)c1ccc(N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 7, 7, 7, 7, 8, 24, 24, 24, 24, 24, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 7, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485533 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485533 Building ZINC001184485580 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485580 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/500 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485580 none O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 12, 12, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 16, 16, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/501 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485580 none O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 17, 17, 17, 17, 17, 17, 17, 17, 19, 19, 17, 17, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485580 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 Building ZINC001184485580 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485580 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 500) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485580 none O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 12, 12, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 16, 16, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 501) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485580 none O=C(N1CCNC(=O)[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 17, 17, 17, 17, 17, 17, 17, 17, 19, 19, 17, 17, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 19, 19, 19, 19, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485580 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485580 Building ZINC001184485585 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485585 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/502 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485585 none O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 18, 18, 18, 18, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/503 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485585 none O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485585 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 Building ZINC001184485585 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485585 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 502) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485585 none O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 18, 18, 18, 18, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 503) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485585 none O=C(N1CCNC(=O)[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485585 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485585 Building ZINC001184485596 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485596 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/504 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485596 none COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 9, 9, 4, 9, 9, 9, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 9, 4, 9, 20, 20, 20, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/505 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485596 none COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 9, 9, 7, 9, 9, 9, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 9, 9, 9, 20, 20, 20, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485596 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 Building ZINC001184485596 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485596 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 504) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485596 none COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 9, 9, 4, 9, 9, 9, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 9, 4, 9, 20, 20, 20, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 505) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485596 none COC(=O)c1cccc(C(=O)OC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 9, 9, 7, 9, 9, 9, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 9, 9, 9, 20, 20, 20, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485596 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485596 Building ZINC001184485649 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485649 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/506 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)nc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1) `ZINC001184485649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485649 none COc1cc(C)nc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 17, 17, 17, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/507 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)nc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1) `ZINC001184485649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485649 none COc1cc(C)nc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 18, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485649 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 Building ZINC001184485649 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485649 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 506) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(C)nc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1) `ZINC001184485649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485649 none COc1cc(C)nc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 17, 17, 17, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 507) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(C)nc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1) `ZINC001184485649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485649 none COc1cc(C)nc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 18, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485649 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485649 Building ZINC001184485709 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485709 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/508 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1) `ZINC001184485709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485709 none CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 30, 21, 21, 21, 21, 21, 19, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 21, 21, 21, 21, 15, 15, 3, 4, 4, 4, 4, 21, 21] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/509 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1) `ZINC001184485709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485709 none CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 16, 28, 16, 16, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 13, 13, 3, 4, 4, 4, 4, 16, 16] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485709 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 Building ZINC001184485709 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485709 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 508) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1) `ZINC001184485709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485709 none CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 30, 21, 21, 21, 21, 21, 19, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 21, 21, 21, 21, 15, 15, 3, 4, 4, 4, 4, 21, 21] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 509) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1) `ZINC001184485709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485709 none CC(C)(C)OC(=O)N1C[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)O[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 16, 28, 16, 16, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 16, 16, 13, 13, 3, 4, 4, 4, 4, 16, 16] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485709 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485709 Building ZINC001184485762 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485762 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/510 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485762 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 23, 34, 23, 23, 23, 23, 23, 17, 14, 23, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 13, 13, 3, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/511 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485762 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 24, 34, 24, 24, 24, 24, 24, 19, 17, 24, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 24, 24, 24, 24, 24, 24, 14, 14, 3, 4, 4, 4, 4, 24, 24] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485762 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 Building ZINC001184485762 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485762 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 510) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485762 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 23, 34, 23, 23, 23, 23, 23, 17, 14, 23, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 13, 13, 3, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 511) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485762 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 24, 34, 24, 24, 24, 24, 24, 19, 17, 24, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 24, 24, 24, 24, 24, 24, 14, 14, 3, 4, 4, 4, 4, 24, 24] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485762 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485762 Building ZINC001184485763 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485763 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/512 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485763 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 24, 35, 24, 24, 24, 24, 24, 19, 17, 24, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 24, 24, 24, 24, 24, 24, 14, 14, 3, 4, 4, 4, 4, 24, 24] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/513 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485763 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 23, 34, 23, 23, 23, 23, 23, 17, 14, 23, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 13, 13, 3, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485763 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 Building ZINC001184485763 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485763 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 512) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485763 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 24, 35, 24, 24, 24, 24, 24, 19, 17, 24, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 24, 24, 24, 24, 24, 24, 14, 14, 3, 4, 4, 4, 4, 24, 24] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 513) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184485763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184485763 none CC(C)(C)OC(=O)N1CC2(C1)CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 23, 34, 23, 23, 23, 23, 23, 17, 14, 23, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 13, 13, 3, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485763 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485763 Building ZINC001184485822 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485822 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/514 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1) `ZINC001184485822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184485822 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 40, 40, 40, 40, 36, 36, 36, 7, 7, 3, 3, 4, 4, 4, 3, 3, 3, 7, 7, 7, 7, 7, 36, 36, 40, 40, 40, 40, 40, 40, 40, 40, 36, 7, 7, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/515 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1) `ZINC001184485822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184485822 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 29, 29, 29, 29, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 29, 29, 29, 29, 29, 27, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485822 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 Building ZINC001184485822 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485822 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 514) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1) `ZINC001184485822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184485822 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36, 40, 40, 40, 40, 36, 36, 36, 7, 7, 3, 3, 4, 4, 4, 3, 3, 3, 7, 7, 7, 7, 7, 36, 36, 40, 40, 40, 40, 40, 40, 40, 40, 36, 7, 7, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 515) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1) `ZINC001184485822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184485822 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4nc5ccc(N6CCCC6)cn5n4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 29, 29, 29, 29, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 29, 29, 29, 29, 29, 27, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485822 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485822 Building ZINC001184485844 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485844 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/516 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485844 none COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/517 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485844 none COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485844 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 Building ZINC001184485844 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485844 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 516) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485844 none COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 517) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184485844 none COc1cc(N2CCN(C(C)=O)CC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485844 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485844 Building ZINC001184485847 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485847 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/518 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F) `ZINC001184485847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184485847 none CS(=O)(=O)c1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 23, 23, 23, 13, 3, 9, 9, 9, 9, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/519 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F) `ZINC001184485847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184485847 none CS(=O)(=O)c1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 23, 23, 23, 13, 3, 9, 9, 9, 9, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485847 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 Building ZINC001184485847 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485847 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 518) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CS(=O)(=O)c1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F) `ZINC001184485847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184485847 none CS(=O)(=O)c1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 23, 23, 23, 13, 3, 9, 9, 9, 9, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 519) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CS(=O)(=O)c1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F) `ZINC001184485847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184485847 none CS(=O)(=O)c1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 23, 23, 23, 13, 3, 9, 9, 9, 9, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485847 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485847 Building ZINC001184485875 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485875 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/520 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 30, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 42, 42, 42, 42] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/521 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 30, 24, 24, 24, 24, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 24, 24, 7, 7, 2, 3, 3, 3, 3, 24, 41, 41, 41, 41] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/522 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/522' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/523 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/523' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485875 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 Building ZINC001184485875 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485875 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 520) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 30, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 42, 42, 42, 42] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 521) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 30, 24, 24, 24, 24, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 24, 24, 7, 7, 2, 3, 3, 3, 3, 24, 41, 41, 41, 41] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 522) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 523) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485875 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 Building ZINC001184485875 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485875 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 520) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 30, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 42, 42, 42, 42] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 521) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 30, 24, 24, 24, 24, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 24, 24, 7, 7, 2, 3, 3, 3, 3, 24, 41, 41, 41, 41] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 522) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 523) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485875 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 Building ZINC001184485875 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485875 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 520) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 30, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 42, 42, 42, 42] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 521) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 30, 24, 24, 24, 24, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 24, 24, 7, 7, 2, 3, 3, 3, 3, 24, 41, 41, 41, 41] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 522) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 523) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1) `ZINC001184485875.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184485875 none C[N@]1CC[N@@](c2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 25, 20, 20, 20, 20, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 7, 7, 3, 3, 3, 3, 3, 20, 40, 40, 40, 40] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184485875 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184485875 Building ZINC001184486200 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486200 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/524 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184486200 none O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 14, 14, 14, 14, 21, 21, 21, 22, 22, 21, 22, 22, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 14, 14, 14, 14, 14, 22, 22, 21, 22, 22, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/525 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184486200 none O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 14, 14, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 14, 14, 14, 14, 14, 22, 22, 22, 22, 22, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486200 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 Building ZINC001184486200 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486200 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 524) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184486200 none O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 14, 14, 14, 14, 21, 21, 21, 22, 22, 21, 22, 22, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 14, 14, 14, 14, 14, 22, 22, 21, 22, 22, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 525) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184486200 none O=C(NC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 14, 14, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 14, 14, 14, 14, 14, 22, 22, 22, 22, 22, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486200 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486200 Building ZINC001184486223 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486223 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/526 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCC1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184486223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184486223 none O=C(NC1CCCC1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 17, 29, 29, 29, 29, 12, 12, 12, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 3, 4, 4, 4, 4, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 97 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/527 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCC1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184486223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184486223 none O=C(NC1CCCC1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 17, 29, 29, 29, 29, 12, 12, 12, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 3, 4, 4, 4, 4, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486223 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 Building ZINC001184486223 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486223 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 526) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCCC1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184486223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184486223 none O=C(NC1CCCC1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 17, 29, 29, 29, 29, 12, 12, 12, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 3, 4, 4, 4, 4, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 97 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 527) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC1CCCC1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184486223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184486223 none O=C(NC1CCCC1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 17, 29, 29, 29, 29, 12, 12, 12, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 3, 4, 4, 4, 4, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486223 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486223 Building ZINC001184486249 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486249 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/528 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486249 none O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 8, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 31, 31, 31, 31, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/529 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486249 none O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 8, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 29, 29, 29, 29, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486249 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 Building ZINC001184486249 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486249 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 528) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486249 none O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 8, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 31, 31, 31, 31, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 529) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486249 none O=C(N1CCN(c2ccc3[nH]ncc3c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 8, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 29, 29, 29, 29, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486249 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486249 Building ZINC001184486258 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486258 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/530 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486258 none O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 25, 25, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/531 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486258 none O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486258 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 Building ZINC001184486258 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486258 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 530) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486258 none O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 25, 25, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 531) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184486258 none O=C(N1CCN(c2nc3ccccc3[nH]2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 28, 28, 28, 28, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486258 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486258 Building ZINC001184486262 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486262 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/532 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NS(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184486262 none CC(C)NS(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 20, 16, 11, 16, 16, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 19, 11, 11, 11, 11, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/533 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NS(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184486262 none CC(C)NS(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 22, 18, 11, 18, 18, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 21, 11, 11, 11, 11, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486262 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 Building ZINC001184486262 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486262 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 532) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(C)NS(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184486262 none CC(C)NS(=O)(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 20, 16, 11, 16, 16, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 19, 11, 11, 11, 11, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 533) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(C)NS(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184486262 none CC(C)NS(=O)(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 22, 18, 11, 18, 18, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 21, 11, 11, 11, 11, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486262 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486262 Building ZINC001184486283 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486283 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/534 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486283 none CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 15, 22, 26, 22, 6, 22, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/535 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486283 none CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 11, 8, 12, 8, 4, 8, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486283 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 Building ZINC001184486283 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486283 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 534) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486283 none CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 15, 22, 26, 22, 6, 22, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 535) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486283 none CC(C)(C)OC(=O)NC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 11, 8, 12, 8, 4, 8, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486283 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486283 Building ZINC001184486299 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486299 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/536 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184486299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486299 none CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 22, 6, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/537 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184486299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486299 none CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 17, 3, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3] 34 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486299 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 Building ZINC001184486299 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486299 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 536) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184486299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486299 none CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 22, 6, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 537) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184486299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184486299 none CCOC(=O)[C@H]1Cn2nccc2[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 17, 3, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3] 34 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486299 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486299 Building ZINC001184486325 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486325 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/538 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184486325 none O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/539 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184486325 none O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486325 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 Building ZINC001184486325 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486325 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 538) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184486325 none O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 539) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184486325 none O=C(N1CCC2(CC1)OC(=O)c1ccncc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486325 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486325 Building ZINC001184486451 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486451 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/540 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486451 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 10, 10, 10, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 35 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 60 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/541 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486451 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 6, 8, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 4] 25 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 33 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486451 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 Building ZINC001184486451 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486451 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 540) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486451 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 10, 10, 10, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 35 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 60 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 541) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486451 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 6, 8, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 4] 25 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 33 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486451 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486451 Building ZINC001184486452 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486452 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/542 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486452 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 8, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 4] 24 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 36 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/543 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486452 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 6, 6, 6, 6, 6, 5, 5, 9, 9, 9, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 5] 22 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 46 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486452 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 Building ZINC001184486452 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486452 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 542) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486452 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 8, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 4] 24 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 36 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 543) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1) `ZINC001184486452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184486452 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N([C@H]3CCC34CCNCC4)S(=O)(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 6, 6, 6, 6, 6, 5, 5, 9, 9, 9, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 5] 22 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 46 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486452 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486452 Building ZINC001184486506 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486506 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/544 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184486506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184486506 none CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 20, 11, 20, 11, 11, 11, 11, 11, 18, 18, 12, 18, 18, 18, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 11, 18, 18, 17, 18, 4, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/545 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184486506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184486506 none CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 11, 19, 11, 11, 11, 11, 11, 18, 18, 17, 18, 18, 18, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 23, 23, 23, 23, 23, 11, 18, 18, 18, 18, 4, 6, 6, 6, 8, 8, 8, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486506 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 Building ZINC001184486506 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486506 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 544) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184486506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184486506 none CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 20, 11, 20, 11, 11, 11, 11, 11, 18, 18, 12, 18, 18, 18, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 11, 18, 18, 17, 18, 4, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 545) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184486506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184486506 none CCOC(=O)c1cnn(c2ccccc2F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 11, 19, 11, 11, 11, 11, 11, 18, 18, 17, 18, 18, 18, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 23, 23, 23, 23, 23, 11, 18, 18, 18, 18, 4, 6, 6, 6, 8, 8, 8, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486506 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486506 Building ZINC001184486557 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486557 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/546 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1) `ZINC001184486557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486557 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 13, 21, 24, 24, 3, 3, 3, 9, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 24, 24, 24, 24, 24, 24, 24, 9, 9, 13, 13, 13, 13, 13, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/547 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1) `ZINC001184486557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486557 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 14, 20, 23, 23, 3, 3, 3, 9, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 23, 23, 23, 23, 23, 23, 23, 9, 9, 13, 13, 13, 13, 13, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486557 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 Building ZINC001184486557 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486557 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 546) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1) `ZINC001184486557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486557 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 13, 21, 24, 24, 3, 3, 3, 9, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 24, 24, 24, 24, 24, 24, 24, 9, 9, 13, 13, 13, 13, 13, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 547) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1) `ZINC001184486557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486557 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4c(c(COC(C)C)nn4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 14, 20, 23, 23, 3, 3, 3, 9, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 23, 23, 23, 23, 23, 23, 23, 9, 9, 13, 13, 13, 13, 13, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486557 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486557 Building ZINC001184486647 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486647 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/548 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O) `ZINC001184486647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486647 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 31, 32, 32, 20, 9, 20, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 4, 8, 8, 8, 8, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/549 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O) `ZINC001184486647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486647 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 29, 20, 9, 20, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 4, 8, 8, 8, 8, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486647 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 Building ZINC001184486647 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486647 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 548) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O) `ZINC001184486647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486647 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 31, 32, 32, 20, 9, 20, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 4, 8, 8, 8, 8, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 549) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O) `ZINC001184486647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486647 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 29, 20, 9, 20, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 4, 8, 8, 8, 8, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486647 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486647 Building ZINC001184486963 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486963 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/550 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184486963 none O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 18, 18, 18, 18, 31, 31, 18, 18, 31, 31, 31, 31, 31, 18, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 31, 31, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/551 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184486963 none O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 13, 13, 13, 13, 31, 31, 13, 13, 31, 31, 31, 31, 31, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 31, 31, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486963 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 Building ZINC001184486963 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486963 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 550) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184486963 none O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 18, 18, 18, 18, 31, 31, 18, 18, 31, 31, 31, 31, 31, 18, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 31, 31, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 551) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184486963 none O=C(N1CCN(c2ncc(C(F)(F)F)cn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 9, 13, 13, 13, 13, 31, 31, 13, 13, 31, 31, 31, 31, 31, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 31, 31, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486963 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486963 Building ZINC001184486969 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486969 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/552 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184486969 none O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 10, 10, 10, 10, 10, 10, 10, 10, 25, 26, 26, 10, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 26, 26, 26, 26, 26, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/553 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184486969 none O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 11, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486969 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 Building ZINC001184486969 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486969 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 552) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184486969 none O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 10, 10, 10, 10, 10, 10, 10, 10, 25, 26, 26, 10, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 26, 26, 26, 26, 26, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 553) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184486969 none O=C(N1CCC2(CCN(CC3CC3)C2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 11, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486969 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486969 Building ZINC001184486974 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486974 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/554 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184486974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184486974 none COc1ccc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 25, 10, 10, 10, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 29, 29] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/555 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184486974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184486974 none COc1ccc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 29, 25, 12, 25, 12, 12, 12, 3, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12, 29, 29] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486974 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 Building ZINC001184486974 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486974 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 554) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184486974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184486974 none COc1ccc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 25, 10, 10, 10, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 29, 29] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 555) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1) `ZINC001184486974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184486974 none COc1ccc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 29, 25, 12, 25, 12, 12, 12, 3, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12, 29, 29] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486974 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486974 Building ZINC001184486992 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486992 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/556 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486992 none O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/557 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486992 none O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 22, 22, 22, 22, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486992 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 Building ZINC001184486992 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486992 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 556) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486992 none O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 557) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486992 none O=C(N1CCC(n2nnc3ccccc3c2=O)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 22, 22, 22, 22, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184486992 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184486992 Building ZINC001184487349 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487349 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/558 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487349 none CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 30, 37, 30, 30, 30, 22, 30, 10, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 37, 37, 37, 37, 37, 37, 37, 37, 37, 30, 30, 30, 30, 10, 10, 7, 7, 3, 4, 4, 4, 4, 30, 30] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/559 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487349 none CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 25, 34, 25, 25, 25, 19, 25, 9, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 25, 25, 25, 25, 9, 9, 6, 6, 3, 4, 4, 4, 4, 25, 25] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487349 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 Building ZINC001184487349 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487349 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 558) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487349 none CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 30, 37, 30, 30, 30, 22, 30, 10, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 37, 37, 37, 37, 37, 37, 37, 37, 37, 30, 30, 30, 30, 10, 10, 7, 7, 3, 4, 4, 4, 4, 30, 30] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 559) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487349 none CC(C)(C)OC(=O)N1CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 25, 34, 25, 25, 25, 19, 25, 9, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 25, 25, 25, 25, 9, 9, 6, 6, 3, 4, 4, 4, 4, 25, 25] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487349 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487349 Building ZINC001184487350 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487350 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/560 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487350 none CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 35, 25, 25, 25, 20, 25, 9, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 25, 25, 9, 9, 6, 6, 3, 4, 4, 4, 4, 25, 25] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/561 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487350 none CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 28, 34, 28, 28, 28, 22, 28, 10, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 34, 34, 34, 34, 34, 34, 34, 34, 34, 28, 28, 28, 28, 10, 10, 7, 7, 3, 4, 4, 4, 4, 28, 28] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487350 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 Building ZINC001184487350 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487350 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 560) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487350 none CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 35, 25, 25, 25, 20, 25, 9, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 25, 25, 9, 9, 6, 6, 3, 4, 4, 4, 4, 25, 25] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 561) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184487350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184487350 none CC(C)(C)OC(=O)N1CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 28, 34, 28, 28, 28, 22, 28, 10, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 34, 34, 34, 34, 34, 34, 34, 34, 34, 28, 28, 28, 28, 10, 10, 7, 7, 3, 4, 4, 4, 4, 28, 28] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487350 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487350 Building ZINC001184487362 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487362 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/562 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(N)CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1) `ZINC001184487362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487362 none CC(C)(N)CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 11, 11, 11, 16, 16, 13, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 16, 16, 11, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/563 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(N)CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1) `ZINC001184487362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487362 none CC(C)(N)CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 12, 6, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 13, 13, 13, 20, 20, 18, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 7, 7, 7, 7, 20, 20, 18, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487362 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 Building ZINC001184487362 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487362 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 562) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(N)CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1) `ZINC001184487362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487362 none CC(C)(N)CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 11, 11, 11, 16, 16, 13, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 16, 16, 11, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 563) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(N)CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1) `ZINC001184487362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487362 none CC(C)(N)CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)S(=O)(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 12, 6, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 13, 13, 13, 20, 20, 18, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 7, 7, 7, 7, 20, 20, 18, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487362 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487362 Building ZINC001184487366 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487366 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/564 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(N2CCCNC2=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184487366 none O=C(NCc1ccc(N2CCCNC2=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 16, 16, 28, 28, 28, 28, 28, 28, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 24, 24, 28, 28, 28, 28, 28, 28, 28, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/565 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(N2CCCNC2=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184487366 none O=C(NCc1ccc(N2CCCNC2=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 16, 16, 34, 34, 34, 34, 34, 34, 27, 27, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 27, 27, 34, 34, 34, 34, 34, 34, 34, 27, 27, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487366 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 Building ZINC001184487366 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487366 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 564) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(NCc1ccc(N2CCCNC2=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184487366 none O=C(NCc1ccc(N2CCCNC2=O)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 16, 16, 28, 28, 28, 28, 28, 28, 24, 24, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 24, 24, 28, 28, 28, 28, 28, 28, 28, 24, 24, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 565) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(NCc1ccc(N2CCCNC2=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184487366 none O=C(NCc1ccc(N2CCCNC2=O)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 16, 16, 34, 34, 34, 34, 34, 34, 27, 27, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 27, 27, 34, 34, 34, 34, 34, 34, 34, 27, 27, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487366 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487366 Building ZINC001184487438 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487438 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/566 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/567 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/568 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/568' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/569 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/569' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487438 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 Building ZINC001184487438 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487438 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 566) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 567) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 568) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 569) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487438 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 Building ZINC001184487438 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487438 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 566) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 567) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 568) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 569) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487438 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 Building ZINC001184487438 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487438 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 566) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 567) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 568) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 13, 13, 13, 13, 21, 26, 26, 21, 26, 26, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 13, 13, 21, 21, 26, 26, 21, 26, 26, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 569) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487438 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 18, 18, 18, 18, 29, 31, 31, 29, 31, 31, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 3, 18, 18, 29, 29, 31, 31, 29, 31, 31, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487438 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487438 Building ZINC001184487441 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487441 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/570 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/571 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/572 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/572' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/573 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/573' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487441 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 Building ZINC001184487441 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487441 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 570) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 571) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 572) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 573) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487441 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 Building ZINC001184487441 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487441 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 570) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 571) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 572) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 573) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487441 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 Building ZINC001184487441 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184487441 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 570) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 571) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 572) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 28, 29, 29, 28, 29, 29, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 17, 17, 28, 28, 29, 29, 28, 29, 29, 17, 17, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 573) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1) `ZINC001184487441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184487441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184487441 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cncnc3[C@@H]3CN(Cc4ccccc4)CCO3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 22, 26, 26, 22, 26, 26, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 14, 14, 22, 22, 26, 26, 22, 26, 26, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487441 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487441 Building ZINC001184487434 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487434 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/574 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1) `ZINC001184487434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487434 none COc1ccnc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 4, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 66 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/575 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1) `ZINC001184487434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487434 none COc1ccnc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 4, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487434 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 Building ZINC001184487434 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487434 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 574) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccnc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1) `ZINC001184487434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487434 none COc1ccnc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 4, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 66 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 575) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccnc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1) `ZINC001184487434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487434 none COc1ccnc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 4, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487434 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487434 Building ZINC001184487461 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487461 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/576 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184487461 none O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 25, 25, 25, 27, 27, 37, 37, 37, 37, 37, 25, 25, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 25, 25, 25, 25, 25, 37, 37, 37, 37, 25, 25, 25, 25, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/577 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184487461 none O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 20, 20, 20, 20, 21, 21, 31, 31, 31, 31, 31, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 20, 20, 20, 20, 20, 31, 31, 31, 31, 20, 20, 20, 20, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487461 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 Building ZINC001184487461 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487461 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 576) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184487461 none O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 25, 25, 25, 27, 27, 37, 37, 37, 37, 37, 25, 25, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 25, 25, 25, 25, 25, 37, 37, 37, 37, 25, 25, 25, 25, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 577) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184487461 none O=C(NCC1CCN(C(=O)c2cccnc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 20, 20, 20, 20, 21, 21, 31, 31, 31, 31, 31, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 20, 20, 20, 20, 20, 31, 31, 31, 31, 20, 20, 20, 20, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487461 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487461 Building ZINC001184487666 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487666 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/578 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184487666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487666 none O=C(Cc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 13, 30, 31, 31, 31, 31, 31, 8, 8, 8, 8, 5, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 30, 30, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 111 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/579 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184487666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487666 none O=C(Cc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 18, 38, 39, 39, 38, 39, 39, 15, 15, 15, 15, 10, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 38, 38, 39, 39, 39, 39, 39, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487666 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 Building ZINC001184487666 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487666 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 578) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Cc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184487666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487666 none O=C(Cc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 13, 30, 31, 31, 31, 31, 31, 8, 8, 8, 8, 5, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 30, 30, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 111 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 579) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Cc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184487666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184487666 none O=C(Cc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 18, 38, 39, 39, 38, 39, 39, 15, 15, 15, 15, 10, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 38, 38, 39, 39, 39, 39, 39, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487666 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487666 Building ZINC001184487676 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487676 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/580 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1cccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1) `ZINC001184487676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184487676 none COCCOc1cccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 14, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 14] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/581 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1cccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1) `ZINC001184487676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184487676 none COCCOc1cccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 15, 48, 48, 48, 48, 48, 48, 48, 15, 15, 15, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487676 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 Building ZINC001184487676 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487676 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 580) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCOc1cccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1) `ZINC001184487676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184487676 none COCCOc1cccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 14, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 14] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 581) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCOc1cccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1) `ZINC001184487676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184487676 none COCCOc1cccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 15, 48, 48, 48, 48, 48, 48, 48, 15, 15, 15, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487676 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487676 Building ZINC001184487697 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487697 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/582 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1) `ZINC001184487697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184487697 none COc1ccnc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 14, 14, 14, 14, 14, 16, 18, 18, 18, 16, 16, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/583 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1) `ZINC001184487697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184487697 none COc1ccnc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 14, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487697 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 Building ZINC001184487697 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487697 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 582) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccnc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1) `ZINC001184487697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184487697 none COc1ccnc(N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 14, 14, 14, 14, 14, 16, 18, 18, 18, 16, 16, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 583) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccnc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1) `ZINC001184487697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184487697 none COc1ccnc(N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C2CCNCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 14, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487697 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487697 Building ZINC001184487717 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487717 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/584 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2ncc(Br)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184487717 none O=C(N1CCn2ncc(Br)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/585 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2ncc(Br)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184487717 none O=C(N1CCn2ncc(Br)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487717 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 Building ZINC001184487717 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487717 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 584) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2ncc(Br)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184487717 none O=C(N1CCn2ncc(Br)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 585) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2ncc(Br)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001184487717 none O=C(N1CCn2ncc(Br)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487717 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487717 Building ZINC001184487755 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487755 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/586 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487755 none O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/587 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487755 none O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487755 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 Building ZINC001184487755 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487755 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 586) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487755 none O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 587) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487755 none O=C(N1CCC2(CC1)OC(=O)c1ncccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487755 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487755 Building ZINC001184487918 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487918 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/588 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1) `ZINC001184487918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184487918 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 24, 24, 24, 31, 31, 24, 24, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 24, 24, 31, 31, 24, 24, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/589 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1) `ZINC001184487918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184487918 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 30, 30, 23, 23, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 30, 30, 23, 23, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487918 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 Building ZINC001184487918 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487918 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 588) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1) `ZINC001184487918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184487918 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 24, 24, 24, 31, 31, 24, 24, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 24, 24, 31, 31, 24, 24, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 589) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1) `ZINC001184487918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184487918 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CCn5c(c6ccc(C(N)=O)cc6)cnc54)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 30, 30, 23, 23, 9, 9, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 30, 30, 23, 23, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001184487918 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001184487918 Building ZINC000110101901 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110101901 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/590 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1) `ZINC000110101901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110101901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000110101901 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 55 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/591 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1) `ZINC000110101901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110101901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000110101901 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 14, 14, 14, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000110101901 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 Building ZINC000110101901 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110101901 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 590) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1) `ZINC000110101901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110101901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000110101901 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 55 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 591) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1) `ZINC000110101901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110101901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000110101901 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C2OCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 14, 14, 14, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000110101901 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000110101901 Building ZINC000776747019 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776747019 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/592 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/592' -> `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)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=O) `ZINC000776747019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000776747019 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 14, 24, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 24, 24, 43, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/593 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/593' -> `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)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=O) `ZINC000776747019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000776747019 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 13, 23, 41, 41, 41, 41, 41, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 23, 23, 41, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000776747019 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 Building ZINC000776747019 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776747019 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 592) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=O) `ZINC000776747019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000776747019 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 14, 24, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 24, 24, 43, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 593) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=O) `ZINC000776747019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000776747019 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2cccc(Cl)c2Cl)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 13, 23, 41, 41, 41, 41, 41, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 23, 23, 41, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000776747019 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776747019 Building ZINC000776859219 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776859219 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/594 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/594' -> `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)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=O) `ZINC000776859219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776859219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000776859219 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 22, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/595 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/595' -> `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)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=O) `ZINC000776859219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776859219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000776859219 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000776859219 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 Building ZINC000776859219 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776859219 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 594) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=O) `ZINC000776859219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776859219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000776859219 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 22, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 595) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=O) `ZINC000776859219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776859219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000776859219 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(C(C)(C)C)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000776859219 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000776859219 Building ZINC000021970690 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000021970690 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/596 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000021970690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000021970690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000021970690 none CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 8, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/597 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000021970690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000021970690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000021970690 none CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 8, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000021970690 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 Building ZINC000021970690 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000021970690 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 596) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000021970690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000021970690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000021970690 none CCOC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 8, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 597) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000021970690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000021970690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000021970690 none CCOC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 8, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000021970690 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000021970690 Building ZINC000027388244 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000027388244 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/598 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1) `ZINC000027388244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000027388244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000027388244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 13, 16, 16, 16, 16, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 2, 2, 2, 2, 4, 13, 13, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/599 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1) `ZINC000027388244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000027388244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000027388244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 10, 12, 12, 12, 12, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000027388244 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 Building ZINC000027388244 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000027388244 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 598) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1) `ZINC000027388244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000027388244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000027388244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 13, 16, 16, 16, 16, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 2, 2, 2, 2, 4, 13, 13, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 599) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1) `ZINC000027388244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000027388244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000027388244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)NCc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 10, 12, 12, 12, 12, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000027388244 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000027388244 Building ZINC000410033005 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410033005 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/600 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)cn1) `ZINC000410033005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410033005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000410033005 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)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.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 32, 32, 32, 7, 32, 32, 32, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 32, 18, 32, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/601 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)cn1) `ZINC000410033005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410033005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000410033005 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)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.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 4, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 29, 29, 29, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000410033005 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 Building ZINC000410033005 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410033005 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 600) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)cn1) `ZINC000410033005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410033005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000410033005 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)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.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 32, 32, 32, 7, 32, 32, 32, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 32, 18, 32, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 601) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)cn1) `ZINC000410033005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410033005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000410033005 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cc(Br)ccc3F)s2)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.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 4, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 29, 29, 29, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000410033005 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000410033005 Building ZINC000561119547 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561119547 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/602 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1) `ZINC000561119547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561119547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561119547 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 18, 18, 11, 13, 33, 33, 50, 50, 50, 50, 50, 50, 50, 18, 18, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 18, 18, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/603 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1) `ZINC000561119547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561119547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561119547 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 10, 11, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 17, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000561119547 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 Building ZINC000561119547 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561119547 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 602) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1) `ZINC000561119547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561119547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561119547 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 18, 18, 11, 13, 33, 33, 50, 50, 50, 50, 50, 50, 50, 18, 18, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 18, 18, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 603) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1) `ZINC000561119547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561119547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561119547 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N=c2cc[nH]cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 10, 11, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 17, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000561119547 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000561119547 Building ZINC000933146435 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000933146435 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/604 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1) `ZINC000933146435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000933146435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000933146435 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 17, 17, 4, 17, 4, 4, 4, 3, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/605 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1) `ZINC000933146435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000933146435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000933146435 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000933146435 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 Building ZINC000933146435 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000933146435 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 604) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1) `ZINC000933146435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000933146435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000933146435 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 17, 17, 4, 17, 4, 4, 4, 3, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 605) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1) `ZINC000933146435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000933146435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000933146435 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nccn2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000933146435 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000933146435 Building ZINC000563460537 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563460537 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/606 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000563460537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563460537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000563460537 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 17, 17, 14, 4, 13, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 4, 17, 17, 17, 17, 31, 31, 31, 31, 31, 31, 17, 17, 17, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 31] 50 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/607 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000563460537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563460537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000563460537 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 14, 4, 14, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 4, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 18, 18, 18, 5, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 33] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000563460537 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 Building ZINC000563460537 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563460537 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 606) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000563460537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563460537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000563460537 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 17, 17, 14, 4, 13, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 4, 17, 17, 17, 17, 31, 31, 31, 31, 31, 31, 17, 17, 17, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 31] 50 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 607) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000563460537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563460537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000563460537 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 14, 4, 14, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 4, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 18, 18, 18, 5, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 33] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000563460537 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000563460537 Building ZINC000566631886 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566631886 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/608 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/609 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/610 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/610' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/611 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/611' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000566631886 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 Building ZINC000566631886 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566631886 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 608) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 609) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 610) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 611) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000566631886 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 Building ZINC000566631886 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566631886 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 608) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 609) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 610) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 611) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000566631886 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 Building ZINC000566631886 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566631886 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 608) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 609) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 42] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 610) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 611) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1) `ZINC000566631886.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566631886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000566631886 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 44] 50 rigid atoms, others: [18, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000566631886 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000566631886 Building ZINC000567251158 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567251158 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/612 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1) `ZINC000567251158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567251158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000567251158 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 8, 8, 10, 24, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 8, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/613 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1) `ZINC000567251158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567251158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000567251158 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 7, 7, 8, 22, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000567251158 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 Building ZINC000567251158 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567251158 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 612) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1) `ZINC000567251158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567251158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000567251158 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 8, 8, 10, 24, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 8, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 613) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1) `ZINC000567251158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567251158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000567251158 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 7, 7, 8, 22, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000567251158 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000567251158 Building ZINC000568415834 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568415834 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/614 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000568415834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568415834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568415834 none CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 19, 39, 39, 39, 39, 39, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 3, 3, 3, 3, 3, 3, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 16] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/615 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000568415834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568415834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568415834 none CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 15, 3, 15, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 21, 42, 42, 42, 42, 42, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 3, 3, 3, 3, 3, 3, 19, 19, 42, 42, 42, 42, 42, 42, 42, 42, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000568415834 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 Building ZINC000568415834 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568415834 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 614) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000568415834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568415834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568415834 none CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 19, 39, 39, 39, 39, 39, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 3, 3, 3, 3, 3, 3, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 16] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 615) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000568415834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568415834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568415834 none CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 15, 3, 15, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 21, 42, 42, 42, 42, 42, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 3, 3, 3, 3, 3, 3, 19, 19, 42, 42, 42, 42, 42, 42, 42, 42, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000568415834 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568415834 Building ZINC000568534823 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568534823 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/616 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1) `ZINC000568534823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568534823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568534823 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 7, 18, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 7, 7, 2, 2, 2, 2, 7, 7, 50] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/617 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1) `ZINC000568534823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568534823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568534823 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 6, 21, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 6, 6, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [54, 55, 20, 53, 22, 23, 24, 25, 26, 27, 28, 29, 30, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000568534823 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 Building ZINC000568534823 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568534823 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 616) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1) `ZINC000568534823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568534823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568534823 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 7, 18, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 7, 7, 2, 2, 2, 2, 7, 7, 50] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 617) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1) `ZINC000568534823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568534823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000568534823 none Cn1cc(c2ccc3c(c2)C(C)(C)CN3C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 6, 21, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 6, 6, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [54, 55, 20, 53, 22, 23, 24, 25, 26, 27, 28, 29, 30, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000568534823 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000568534823 Building ZINC000569869484 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000569869484 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/618 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/619 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/620 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/620' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/621 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/621' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000569869484 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 Building ZINC000569869484 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000569869484 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 618) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 619) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 620) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 621) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000569869484 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 Building ZINC000569869484 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000569869484 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 618) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 619) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 620) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 621) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000569869484 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 Building ZINC000569869484 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000569869484 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 618) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 619) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 36, 36, 36, 36, 36, 36, 13, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 13, 13, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 41] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 620) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 621) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1) `ZINC000569869484.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000569869484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000569869484 none Cn1cc(c2ccc3c(c2)N(CC2CN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 12, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 3, 35, 35, 35, 35, 42, 42, 42, 42, 42, 42, 35, 35, 35, 12, 12, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 42] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000569869484 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000569869484 Building ZINC000575197243 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000575197243 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/622 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1) `ZINC000575197243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000575197243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000575197243 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 26, 7, 24, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 8, 7, 7, 2, 2, 2, 2, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/623 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1) `ZINC000575197243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000575197243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000575197243 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 24, 6, 23, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 8, 6, 6, 2, 2, 2, 2, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000575197243 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 Building ZINC000575197243 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000575197243 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 622) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1) `ZINC000575197243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000575197243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000575197243 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 26, 7, 24, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 8, 7, 7, 2, 2, 2, 2, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 623) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1) `ZINC000575197243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000575197243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000575197243 none Cn1cc(c2ccc3c(c2)N(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c4ccc(F)cc4)C2)CC3(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 24, 6, 23, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 8, 6, 6, 2, 2, 2, 2, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000575197243 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000575197243 Building ZINC000576838125 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000576838125 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/624 `/scratch/xiaobo/236261/xbz-8058088.52/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)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)C2)cn1) `ZINC000576838125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000576838125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000576838125 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 32, 32, 10, 10, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 32, 32, 32, 32, 32, 10, 4, 4, 4] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/625 `/scratch/xiaobo/236261/xbz-8058088.52/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)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)C2)cn1) `ZINC000576838125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000576838125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000576838125 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 5, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 34, 34, 13, 13, 4, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 34, 34, 34, 34, 34, 13, 4, 4, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000576838125 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 Building ZINC000576838125 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000576838125 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 624) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)C2)cn1) `ZINC000576838125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000576838125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000576838125 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 32, 32, 10, 10, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 32, 32, 32, 32, 32, 10, 4, 4, 4] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 625) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)C2)cn1) `ZINC000576838125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000576838125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000576838125 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(NC5CC5)cc43)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 5, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 34, 34, 13, 13, 4, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 34, 34, 34, 34, 34, 13, 4, 4, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000576838125 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000576838125 Building ZINC000577747908 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577747908 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/626 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1) `ZINC000577747908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577747908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000577747908 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 8, 21, 21, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 6, 6, 1, 1] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 7, 2, 3, 32, 4, 6, 60, 61, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/627 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1) `ZINC000577747908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577747908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000577747908 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 7, 7, 9, 19, 20, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000577747908 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 Building ZINC000577747908 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577747908 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 626) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1) `ZINC000577747908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577747908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000577747908 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 8, 21, 21, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 6, 6, 1, 1] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 7, 2, 3, 32, 4, 6, 60, 61, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 627) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1) `ZINC000577747908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577747908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000577747908 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 7, 7, 9, 19, 20, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000577747908 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000577747908 Building ZINC000578340083 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000578340083 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/628 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000578340083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000578340083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000578340083 none CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 9, 8, 9, 9, 22, 22, 22, 27, 27, 27, 27, 24, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/629 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000578340083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000578340083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000578340083 none CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 9, 8, 9, 9, 22, 22, 22, 27, 27, 27, 27, 24, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000578340083 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 Building ZINC000578340083 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000578340083 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 628) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000578340083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000578340083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000578340083 none CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 9, 8, 9, 9, 22, 22, 22, 27, 27, 27, 27, 24, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 629) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000578340083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000578340083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000578340083 none CN(C)c1ccc(S(=O)(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 9, 8, 9, 9, 22, 22, 22, 27, 27, 27, 27, 24, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000578340083 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000578340083 Building ZINC000634532508 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000634532508 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/630 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1) `ZINC000634532508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000634532508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000634532508 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 16, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 16, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/631 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1) `ZINC000634532508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000634532508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000634532508 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000634532508 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 Building ZINC000634532508 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000634532508 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 630) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1) `ZINC000634532508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000634532508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000634532508 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 16, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 16, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 631) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1) `ZINC000634532508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000634532508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000634532508 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCO4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000634532508 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000634532508 Building ZINC000637255009 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000637255009 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/632 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2) `ZINC000637255009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000637255009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000637255009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 8, 8, 6, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/633 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2) `ZINC000637255009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000637255009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000637255009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 8, 8, 6, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 5, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000637255009 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 Building ZINC000637255009 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000637255009 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 632) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2) `ZINC000637255009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000637255009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000637255009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 8, 8, 6, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 633) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2) `ZINC000637255009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000637255009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000637255009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 8, 8, 6, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 5, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000637255009 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000637255009 Building ZINC000641237380 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641237380 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/634 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1) `ZINC000641237380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641237380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000641237380 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 11, 11, 12, 12, 10, 10, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/635 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1) `ZINC000641237380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641237380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000641237380 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 12, 12, 15, 15, 10, 10, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 2, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000641237380 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 Building ZINC000641237380 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641237380 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 634) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1) `ZINC000641237380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641237380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000641237380 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 11, 11, 12, 12, 10, 10, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 635) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1) `ZINC000641237380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641237380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000641237380 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 12, 12, 15, 15, 10, 10, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 2, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000641237380 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641237380 Building ZINC000641885547 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641885547 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/636 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1) `ZINC000641885547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641885547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000641885547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/637 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1) `ZINC000641885547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641885547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000641885547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 8, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 3, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 10, 10, 9, 10, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 38 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000641885547 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 Building ZINC000641885547 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641885547 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 636) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1) `ZINC000641885547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641885547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000641885547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 637) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1) `ZINC000641885547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641885547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000641885547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 8, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 3, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 10, 10, 9, 10, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 38 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000641885547 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641885547 Building ZINC000641947009 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641947009 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/638 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1) `ZINC000641947009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641947009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000641947009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 8, 14, 14, 14, 14, 14, 14, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 4, 4, 8, 8, 14, 14, 14, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/639 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1) `ZINC000641947009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641947009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000641947009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 8, 14, 14, 14, 14, 14, 14, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 4, 4, 8, 8, 14, 14, 14, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000641947009 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 Building ZINC000641947009 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641947009 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 638) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1) `ZINC000641947009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641947009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000641947009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 8, 14, 14, 14, 14, 14, 14, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 4, 4, 8, 8, 14, 14, 14, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 639) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1) `ZINC000641947009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641947009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000641947009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 8, 14, 14, 14, 14, 14, 14, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 4, 4, 8, 8, 14, 14, 14, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000641947009 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000641947009 Building ZINC000642149281 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642149281 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/640 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1) `ZINC000642149281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642149281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000642149281 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 32, 32, 32, 32, 32, 37, 37, 37, 37, 32, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 32, 32, 32, 37, 32, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/641 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1) `ZINC000642149281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642149281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000642149281 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 31, 31, 31, 31, 31, 36, 36, 36, 36, 31, 4, 4, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 2, 31, 31, 31, 36, 31, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642149281 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 Building ZINC000642149281 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642149281 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 640) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1) `ZINC000642149281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642149281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000642149281 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 32, 32, 32, 32, 32, 37, 37, 37, 37, 32, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 32, 32, 32, 37, 32, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 641) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1) `ZINC000642149281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642149281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000642149281 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(n3cnnn3)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 31, 31, 31, 31, 31, 36, 36, 36, 36, 31, 4, 4, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 2, 31, 31, 31, 36, 31, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642149281 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642149281 Building ZINC000642180402 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642180402 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/642 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642180402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180402 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 11, 11, 11, 11, 11, 11, 11, 4, 4, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 4, 4, 11, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/643 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642180402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180402 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 4, 4, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 12, 12, 12, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642180402 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 Building ZINC000642180402 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642180402 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 642) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642180402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180402 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 11, 11, 11, 11, 11, 11, 11, 4, 4, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 4, 4, 11, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 643) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642180402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180402 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 4, 4, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 12, 12, 12, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642180402 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180402 Building ZINC000642180403 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642180403 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/644 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642180403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180403 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 13, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 2, 4, 4, 13, 13, 13, 13, 13, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/645 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642180403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180403 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 4, 4, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642180403 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 Building ZINC000642180403 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642180403 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 644) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642180403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180403 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 13, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 2, 4, 4, 13, 13, 13, 13, 13, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 645) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1) `ZINC000642180403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642180403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000642180403 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc([C@]2(C)NC(=O)NC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 4, 4, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642180403 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642180403 Building ZINC000642239130 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642239130 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/646 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642239130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239130 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 12, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 11, 11, 11, 11, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/647 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642239130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239130 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 10, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 9, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642239130 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 Building ZINC000642239130 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642239130 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 646) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642239130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239130 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 12, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 11, 11, 11, 11, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 647) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642239130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239130 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 10, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 9, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642239130 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239130 Building ZINC000642239131 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642239131 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/648 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642239131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239131 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 5, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 9, 10, 10, 10, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/649 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642239131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239131 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 6, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 10, 10, 10, 10, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642239131 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 Building ZINC000642239131 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642239131 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 648) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642239131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239131 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 5, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 9, 10, 10, 10, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 649) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC) `ZINC000642239131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642239131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239131 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 6, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 10, 10, 10, 10, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642239131 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239131 Building ZINC000642239132 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642239132 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/650 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC) `ZINC000642239132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642239132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239132 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 10, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 9, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/651 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC) `ZINC000642239132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642239132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239132 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 12, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 11, 12, 12, 12, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642239132 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 Building ZINC000642239132 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642239132 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 650) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC) `ZINC000642239132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642239132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239132 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 10, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 9, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 651) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC) `ZINC000642239132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642239132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000642239132 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(C(=O)N2[C@H](C)CCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 12, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 11, 12, 12, 12, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642239132 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642239132 Building ZINC000642271365 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642271365 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/652 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1) `ZINC000642271365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642271365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271365 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 15, 5, 5, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/653 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1) `ZINC000642271365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642271365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271365 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 12, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 7, 7, 27, 12, 12, 19, 19, 19, 19, 19] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642271365 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 Building ZINC000642271365 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642271365 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 652) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1) `ZINC000642271365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642271365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271365 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 15, 5, 5, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 653) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1) `ZINC000642271365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642271365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271365 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 12, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 7, 7, 27, 12, 12, 19, 19, 19, 19, 19] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642271365 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271365 Building ZINC000642271366 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642271366 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/654 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1) `ZINC000642271366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642271366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271366 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 9, 16, 17, 17, 16, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 24, 9, 9, 17, 17, 16, 17, 17] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/655 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1) `ZINC000642271366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642271366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271366 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 5, 5, 18, 6, 6, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642271366 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 Building ZINC000642271366 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642271366 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 654) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1) `ZINC000642271366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642271366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271366 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 9, 16, 17, 17, 16, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 24, 9, 9, 17, 17, 16, 17, 17] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 655) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1) `ZINC000642271366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642271366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000642271366 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 5, 5, 18, 6, 6, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642271366 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642271366 Building ZINC000642285234 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642285234 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/656 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 108 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/657 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 6, 6, 6, 4, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 6, 4, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 109 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/658 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/658' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 33, 33, 33, 33] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 104 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/659 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/659' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642285234 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 Building ZINC000642285234 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642285234 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 656) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 108 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 657) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 6, 6, 6, 4, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 6, 4, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 109 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 658) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 33, 33, 33, 33] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 104 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 659) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642285234 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 Building ZINC000642285234 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642285234 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 656) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 108 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 657) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 6, 6, 6, 4, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 6, 4, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 109 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 658) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 33, 33, 33, 33] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 104 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 659) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642285234 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 Building ZINC000642285234 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642285234 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 656) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 108 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 657) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 6, 6, 6, 4, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 6, 4, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 109 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 658) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 33, 33, 33, 33] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 104 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 659) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000642285234.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642285234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642285234 none CC[N@]1CC[N@@](Cc2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 32, 32, 32, 32] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642285234 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642285234 Building ZINC000642769304 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642769304 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/660 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 3, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 43, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 43, 43, 43] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/661 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 20, 6, 6, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 44, 45, 45, 45, 45, 45, 45, 44, 45, 44, 45, 19, 21, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 44, 45, 45, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/662 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/662' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 20, 5, 3, 13, 12, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 13, 13, 44, 44, 45, 45, 45, 45, 45, 45, 43, 43, 45, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 13, 13, 44, 45, 44, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/663 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/663' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 42, 18, 3, 4, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 42, 42, 44, 44, 44, 44, 42, 43, 42, 42, 42, 17, 17, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 42, 42, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642769304 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 Building ZINC000642769304 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642769304 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 660) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 3, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 43, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 43, 43, 43] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 661) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 20, 6, 6, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 44, 45, 45, 45, 45, 45, 45, 44, 45, 44, 45, 19, 21, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 44, 45, 45, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 662) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 20, 5, 3, 13, 12, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 13, 13, 44, 44, 45, 45, 45, 45, 45, 45, 43, 43, 45, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 13, 13, 44, 45, 44, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 663) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 42, 18, 3, 4, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 42, 42, 44, 44, 44, 44, 42, 43, 42, 42, 42, 17, 17, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 42, 42, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642769304 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 Building ZINC000642769304 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642769304 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 660) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 3, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 43, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 43, 43, 43] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 661) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 20, 6, 6, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 44, 45, 45, 45, 45, 45, 45, 44, 45, 44, 45, 19, 21, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 44, 45, 45, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 662) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 20, 5, 3, 13, 12, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 13, 13, 44, 44, 45, 45, 45, 45, 45, 45, 43, 43, 45, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 13, 13, 44, 45, 44, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 663) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 42, 18, 3, 4, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 42, 42, 44, 44, 44, 44, 42, 43, 42, 42, 42, 17, 17, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 42, 42, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642769304 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 Building ZINC000642769304 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000642769304 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 660) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 3, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 43, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 43, 43, 43] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 661) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 20, 6, 6, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 44, 45, 45, 45, 45, 45, 45, 44, 45, 44, 45, 19, 21, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 44, 45, 45, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 662) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 20, 5, 3, 13, 12, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 13, 13, 44, 44, 45, 45, 45, 45, 45, 45, 43, 43, 45, 20, 20, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 13, 13, 44, 45, 44, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 663) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1) `ZINC000642769304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000642769304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000642769304 none CC[N@]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 42, 18, 3, 4, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 13, 13, 42, 42, 44, 44, 44, 44, 42, 43, 42, 42, 42, 17, 17, 13, 13, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 13, 13, 42, 42, 42, 44] 50 rigid atoms, others: [17, 11, 12, 13, 14, 15, 16, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000642769304 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000642769304 Building ZINC000645090735 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645090735 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/664 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000645090735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645090735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000645090735 none CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 16, 27, 31, 31, 29, 31, 31, 4, 16, 16, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 33, 33, 33, 33, 33, 31, 31, 29, 31, 31, 4, 4, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/665 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000645090735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645090735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000645090735 none CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 16, 26, 30, 30, 29, 30, 30, 4, 16, 16, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 32, 32, 32, 32, 32, 30, 30, 29, 30, 30, 4, 4, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000645090735 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 Building ZINC000645090735 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645090735 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 664) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000645090735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645090735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000645090735 none CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 16, 27, 31, 31, 29, 31, 31, 4, 16, 16, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 33, 33, 33, 33, 33, 31, 31, 29, 31, 31, 4, 4, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 665) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000645090735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645090735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000645090735 none CCN(c1ccccc1)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 16, 26, 30, 30, 29, 30, 30, 4, 16, 16, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 32, 32, 32, 32, 32, 30, 30, 29, 30, 30, 4, 4, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000645090735 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000645090735 Building ZINC000647037573 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647037573 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/666 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/666' -> `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)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1) `ZINC000647037573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647037573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000647037573 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 19, 19, 9, 19, 19, 9, 9, 9, 9, 23, 37, 38, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 11, 19, 19, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/667 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/667' -> `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)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1) `ZINC000647037573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647037573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000647037573 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 20, 20, 9, 20, 20, 9, 9, 9, 9, 22, 37, 38, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 15, 20, 20, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000647037573 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 Building ZINC000647037573 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647037573 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 666) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1) `ZINC000647037573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647037573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000647037573 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 19, 19, 9, 19, 19, 9, 9, 9, 9, 23, 37, 38, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 11, 19, 19, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 667) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1) `ZINC000647037573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647037573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000647037573 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sc(c2ccccc2)c(C)c1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 9, 20, 20, 9, 20, 20, 9, 9, 9, 9, 22, 37, 38, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 15, 20, 20, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000647037573 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000647037573 Building ZINC000648033916 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648033916 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/668 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648033916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648033916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648033916 none CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 25, 35, 2, 16, 16, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 36, 36, 36, 36, 36, 35, 35, 35, 35, 35, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/669 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648033916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648033916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648033916 none CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 35, 5, 15, 15, 3, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 34, 34, 34, 34, 34, 35, 35, 35, 35, 35, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648033916 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 Building ZINC000648033916 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648033916 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 668) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648033916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648033916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648033916 none CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 25, 35, 2, 16, 16, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 36, 36, 36, 36, 36, 35, 35, 35, 35, 35, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 669) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648033916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648033916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648033916 none CCN(CC)S(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 35, 5, 15, 15, 3, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 34, 34, 34, 34, 34, 35, 35, 35, 35, 35, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648033916 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648033916 Building ZINC000648034591 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648034591 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/670 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1) `ZINC000648034591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648034591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000648034591 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 14, 4, 10, 14, 14, 35, 35, 35, 36, 36, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 14, 14, 36, 36, 36, 36, 36, 36, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/671 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1) `ZINC000648034591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648034591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000648034591 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 14, 3, 4, 14, 14, 36, 36, 36, 37, 37, 14, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 3, 14, 14, 37, 37, 37, 37, 37, 37, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648034591 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 Building ZINC000648034591 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648034591 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 670) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1) `ZINC000648034591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648034591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000648034591 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 14, 4, 10, 14, 14, 35, 35, 35, 36, 36, 14, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 14, 14, 36, 36, 36, 36, 36, 36, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 671) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1) `ZINC000648034591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648034591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000648034591 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(S(=O)(=O)N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 14, 3, 4, 14, 14, 36, 36, 36, 37, 37, 14, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 3, 14, 14, 37, 37, 37, 37, 37, 37, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648034591 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648034591 Building ZINC000648036219 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648036219 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/672 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648036219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648036219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000648036219 none CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 42, 42, 26, 5, 5, 2, 5, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 3, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 35, 35, 26, 26, 5, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 3] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/673 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648036219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648036219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000648036219 none CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 34, 41, 41, 25, 4, 4, 2, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 34, 34, 25, 25, 4, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648036219 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 Building ZINC000648036219 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648036219 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 672) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648036219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648036219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000648036219 none CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 42, 42, 26, 5, 5, 2, 5, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 3, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 35, 35, 26, 26, 5, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 3] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 673) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648036219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648036219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000648036219 none CCN(CC)CCNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 34, 41, 41, 25, 4, 4, 2, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 34, 34, 25, 25, 4, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648036219 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648036219 Building ZINC000648048010 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648048010 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/674 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1) `ZINC000648048010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648048010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048010 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 25, 25, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/675 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1) `ZINC000648048010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648048010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048010 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 26, 26, 28, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648048010 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 Building ZINC000648048010 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648048010 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 674) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1) `ZINC000648048010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648048010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048010 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 25, 25, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 675) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1) `ZINC000648048010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648048010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048010 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 26, 26, 28, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648048010 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048010 Building ZINC000648048012 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648048012 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/676 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1) `ZINC000648048012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648048012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048012 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 24, 24, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/677 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1) `ZINC000648048012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648048012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048012 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 24, 24, 26, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648048012 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 Building ZINC000648048012 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648048012 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 676) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1) `ZINC000648048012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648048012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048012 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 24, 24, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 677) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1) `ZINC000648048012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648048012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648048012 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2C[C@H](C)O[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 24, 24, 26, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648048012 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648048012 Building ZINC000648053040 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648053040 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/678 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000648053040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648053040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000648053040 none CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 17, 26, 31, 4, 17, 17, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 30, 30, 30, 30, 30, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/679 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000648053040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648053040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000648053040 none CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 16, 25, 29, 4, 16, 16, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648053040 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 Building ZINC000648053040 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648053040 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 678) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000648053040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648053040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000648053040 none CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 17, 26, 31, 4, 17, 17, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 30, 30, 30, 30, 30, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 679) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000648053040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648053040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000648053040 none CCN(CC)S(=O)(=O)c1ccc(N(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 16, 25, 29, 4, 16, 16, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648053040 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648053040 Building ZINC000648058222 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648058222 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/680 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1) `ZINC000648058222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648058222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000648058222 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 14, 11, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 49 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/681 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1) `ZINC000648058222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648058222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000648058222 none CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 14, 11, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 5, 5, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 57 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648058222 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 Building ZINC000648058222 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648058222 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 680) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1) `ZINC000648058222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648058222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000648058222 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 14, 11, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 49 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 681) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1) `ZINC000648058222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648058222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000648058222 none CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 14, 11, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 5, 5, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 57 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648058222 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648058222 Building ZINC000648063604 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648063604 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/682 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1) `ZINC000648063604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648063604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648063604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 21, 21, 21, 39, 39, 39, 39, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/683 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1) `ZINC000648063604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648063604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648063604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 23, 23, 23, 41, 41, 41, 41, 5, 5, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648063604 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 Building ZINC000648063604 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648063604 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 682) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1) `ZINC000648063604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648063604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648063604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 21, 21, 21, 39, 39, 39, 39, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 683) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1) `ZINC000648063604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648063604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648063604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N(C)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 23, 23, 23, 41, 41, 41, 41, 5, 5, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648063604 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648063604 Building ZINC000648302211 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648302211 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/684 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C) `ZINC000648302211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648302211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000648302211 none CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 27, 27, 27, 20, 9, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 33, 33, 33, 33, 33, 33, 18, 16, 14, 14, 11, 11, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/685 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C) `ZINC000648302211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648302211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000648302211 none CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 20, 9, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 23, 23, 29, 29, 29, 32, 32, 32, 18, 17, 14, 14, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 29, 29, 29, 29, 29, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648302211 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 Building ZINC000648302211 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648302211 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 684) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C) `ZINC000648302211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648302211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000648302211 none CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 27, 27, 27, 20, 9, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 33, 33, 33, 33, 33, 33, 18, 16, 14, 14, 11, 11, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 685) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C) `ZINC000648302211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648302211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000648302211 none CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 20, 9, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 23, 23, 29, 29, 29, 32, 32, 32, 18, 17, 14, 14, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 29, 29, 29, 29, 29, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648302211 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648302211 Building ZINC000648405387 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648405387 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/686 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648405387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405387 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 3, 3, 1, 1, 1, 3, 7, 7, 7, 7, 7, 8, 26, 26, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 13, 13, 6, 13, 13, 3, 3, 3, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/687 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648405387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405387 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 26, 26, 38, 38, 38, 38, 38, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 10, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648405387 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 Building ZINC000648405387 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648405387 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 686) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648405387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405387 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 3, 3, 1, 1, 1, 3, 7, 7, 7, 7, 7, 8, 26, 26, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 13, 13, 6, 13, 13, 3, 3, 3, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 687) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648405387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405387 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 26, 26, 38, 38, 38, 38, 38, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 10, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648405387 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405387 Building ZINC000648405388 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648405388 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/688 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648405388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 9, 10, 11, 11, 11, 11, 23, 23, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 107 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/689 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648405388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 3, 8, 8, 10, 10, 10, 11, 28, 28, 42, 42, 42, 42, 42, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 10, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 107 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648405388 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 Building ZINC000648405388 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648405388 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 688) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648405388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405388 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 9, 10, 11, 11, 11, 11, 23, 23, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 107 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 689) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21) `ZINC000648405388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648405388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000648405388 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCCCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 3, 8, 8, 10, 10, 10, 11, 28, 28, 42, 42, 42, 42, 42, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 10, 10, 10, 10, 10, 4, 4, 4, 10, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 107 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648405388 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648405388 Building ZINC000648509202 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648509202 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/690 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1) `ZINC000648509202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648509202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648509202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/691 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1) `ZINC000648509202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648509202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648509202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 6, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 5, 9, 9, 9, 9, 9, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648509202 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 Building ZINC000648509202 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648509202 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 690) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1) `ZINC000648509202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648509202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648509202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 691) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1) `ZINC000648509202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648509202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000648509202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cccnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 6, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 5, 9, 9, 9, 9, 9, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000648509202 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000648509202 Building ZINC000748344608 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748344608 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/692 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000748344608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748344608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000748344608 none CCOC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 9, 6, 9, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/693 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000748344608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748344608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000748344608 none CCOC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 6, 9, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 6, 6, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000748344608 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 Building ZINC000748344608 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748344608 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 692) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000748344608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748344608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000748344608 none CCOC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 9, 6, 9, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 693) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000748344608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748344608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000748344608 none CCOC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 6, 9, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 6, 6, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000748344608 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748344608 Building ZINC000748523857 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748523857 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/694 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1) `ZINC000748523857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748523857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000748523857 none COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 26, 26, 25, 16, 6, 16, 16, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 4, 10, 20, 20, 20, 20, 20, 26, 26, 26, 26, 26, 26, 26, 25, 6, 2, 4, 4, 4, 4, 4, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 26, 26] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/695 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1) `ZINC000748523857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748523857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000748523857 none COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 26, 26, 25, 16, 6, 16, 16, 6, 6, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 2, 4, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 25, 6, 2, 5, 5, 5, 5, 5, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 26, 26] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000748523857 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 Building ZINC000748523857 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748523857 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 694) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1) `ZINC000748523857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748523857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000748523857 none COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 26, 26, 25, 16, 6, 16, 16, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 4, 10, 20, 20, 20, 20, 20, 26, 26, 26, 26, 26, 26, 26, 25, 6, 2, 4, 4, 4, 4, 4, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 26, 26] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 695) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1) `ZINC000748523857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748523857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000748523857 none COc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 26, 26, 25, 16, 6, 16, 16, 6, 6, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 2, 4, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 25, 6, 2, 5, 5, 5, 5, 5, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 26, 26] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000748523857 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000748523857 Building ZINC000679001377 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679001377 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/696 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/696' -> `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(CC(=O)Nc1ccccc1Br)Cc1ccco1) `ZINC000679001377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679001377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000679001377 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1Br)Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 10, 15, 15, 15, 25, 25, 15, 25, 25, 25, 5, 10, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 15, 25, 25, 24, 25, 10, 10, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/697 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/697' -> `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(CC(=O)Nc1ccccc1Br)Cc1ccco1) `ZINC000679001377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679001377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000679001377 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1Br)Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 9, 13, 13, 13, 23, 23, 13, 23, 23, 23, 4, 8, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 13, 23, 23, 22, 23, 8, 8, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000679001377 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 Building ZINC000679001377 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679001377 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 696) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1Br)Cc1ccco1) `ZINC000679001377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679001377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000679001377 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1Br)Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 10, 15, 15, 15, 25, 25, 15, 25, 25, 25, 5, 10, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 15, 25, 25, 24, 25, 10, 10, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 697) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1Br)Cc1ccco1) `ZINC000679001377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679001377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000679001377 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(=O)Nc1ccccc1Br)Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 9, 13, 13, 13, 23, 23, 13, 23, 23, 23, 4, 8, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 13, 23, 23, 22, 23, 8, 8, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000679001377 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679001377 Building ZINC000679006680 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679006680 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/698 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1) `ZINC000679006680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679006680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006680 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 8, 13, 16, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 12, 12, 12, 12, 12, 11, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/699 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1) `ZINC000679006680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679006680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006680 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 9, 15, 15, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 10, 10, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000679006680 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 Building ZINC000679006680 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679006680 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 698) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1) `ZINC000679006680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679006680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006680 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 8, 13, 16, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 12, 12, 12, 12, 12, 11, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 699) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1) `ZINC000679006680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679006680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006680 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 9, 15, 15, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 10, 10, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000679006680 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006680 Building ZINC000679006689 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679006689 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/700 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1) `ZINC000679006689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679006689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006689 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 8, 13, 15, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 10, 10, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/701 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1) `ZINC000679006689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679006689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006689 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 15, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 7, 7, 4, 7, 2, 2, 2, 2, 9, 9, 12, 12, 14, 15, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000679006689 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 Building ZINC000679006689 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679006689 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 700) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1) `ZINC000679006689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679006689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006689 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 8, 13, 15, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 10, 10, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 701) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1) `ZINC000679006689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679006689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679006689 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 15, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 7, 7, 4, 7, 2, 2, 2, 2, 9, 9, 12, 12, 14, 15, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000679006689 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000679006689 Building ZINC000680015581 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680015581 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/702 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1) `ZINC000680015581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680015581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680015581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 7, 9, 9, 9, 9, 9, 4, 4, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 4, 4, 4, 4, 7, 7, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/703 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1) `ZINC000680015581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680015581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680015581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 9, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 5, 5, 5, 5, 9, 9, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680015581 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 Building ZINC000680015581 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680015581 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 702) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1) `ZINC000680015581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680015581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680015581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 7, 9, 9, 9, 9, 9, 4, 4, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 4, 4, 4, 4, 7, 7, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 703) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1) `ZINC000680015581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680015581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680015581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 9, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 5, 5, 5, 5, 9, 9, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680015581 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680015581 Building ZINC000680516254 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680516254 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/704 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000680516254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680516254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000680516254 none Cc1cc(NC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 10, 10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 13, 13, 13, 13, 13, 13, 10, 8, 8, 4, 4, 4, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/705 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000680516254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680516254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000680516254 none Cc1cc(NC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 10, 10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 13, 13, 13, 13, 13, 13, 10, 8, 8, 4, 4, 4, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680516254 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 Building ZINC000680516254 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680516254 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 704) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cc(NC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000680516254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680516254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000680516254 none Cc1cc(NC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 10, 10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 13, 13, 13, 13, 13, 13, 10, 8, 8, 4, 4, 4, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 705) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cc(NC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000680516254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680516254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000680516254 none Cc1cc(NC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 10, 10, 8, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 13, 13, 13, 13, 13, 13, 10, 8, 8, 4, 4, 4, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680516254 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680516254 Building ZINC000680571886 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680571886 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/706 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1) `ZINC000680571886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680571886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680571886 none Cc1cc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 9, 9, 9, 9, 9, 9, 5, 5, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/707 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1) `ZINC000680571886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680571886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680571886 none Cc1cc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 7, 7, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680571886 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 Building ZINC000680571886 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680571886 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 706) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1) `ZINC000680571886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680571886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680571886 none Cc1cc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 9, 9, 9, 9, 9, 9, 5, 5, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 707) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1) `ZINC000680571886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680571886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000680571886 none Cc1cc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 7, 7, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680571886 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680571886 Building ZINC000680674096 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680674096 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/708 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1) `ZINC000680674096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680674096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000680674096 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 27, 27, 16, 7, 4, 7, 7, 4, 4, 4, 4, 4, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 27, 27, 34, 34, 34, 34, 34, 27, 27, 16, 4, 4, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 27, 27] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/709 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1) `ZINC000680674096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680674096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000680674096 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 16, 24, 24, 16, 6, 4, 6, 6, 4, 2, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 32, 32, 32, 32, 32, 24, 24, 16, 4, 4, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680674096 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 Building ZINC000680674096 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680674096 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 708) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1) `ZINC000680674096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680674096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000680674096 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 27, 27, 16, 7, 4, 7, 7, 4, 4, 4, 4, 4, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 27, 27, 34, 34, 34, 34, 34, 27, 27, 16, 4, 4, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 27, 27] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 709) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1) `ZINC000680674096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680674096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000680674096 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 16, 24, 24, 16, 6, 4, 6, 6, 4, 2, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 32, 32, 32, 32, 32, 24, 24, 16, 4, 4, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680674096 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680674096 Building ZINC000680725690 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680725690 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/710 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680725690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725690 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 12, 12, 12, 9, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 4, 4, 4, 9, 9, 9, 12, 12, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/711 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680725690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725690 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 10, 12, 12, 12, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 5, 10, 10, 10, 12, 12, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680725690 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 Building ZINC000680725690 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680725690 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 710) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680725690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725690 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 12, 12, 12, 9, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 4, 4, 4, 9, 9, 9, 12, 12, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 711) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680725690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725690 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 10, 12, 12, 12, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 5, 10, 10, 10, 12, 12, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680725690 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725690 Building ZINC000680725691 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680725691 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/712 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680725691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725691 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 4, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 4, 4, 4, 10, 10, 4, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/713 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680725691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725691 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 9, 9, 4, 9, 9, 12, 12, 12, 9, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 4, 4, 4, 9, 9, 4, 12, 12, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680725691 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 Building ZINC000680725691 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680725691 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 712) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680725691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725691 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 4, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 4, 4, 4, 10, 10, 4, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 713) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1) `ZINC000680725691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680725691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000680725691 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 9, 9, 4, 9, 9, 12, 12, 12, 9, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 4, 4, 4, 9, 9, 4, 12, 12, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680725691 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680725691 Building ZINC000680731429 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680731429 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/714 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680731429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731429 none CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/715 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680731429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731429 none CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 3, 3, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680731429 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 Building ZINC000680731429 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680731429 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 714) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680731429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731429 none CNC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 715) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680731429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731429 none CNC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 3, 3, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680731429 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731429 Building ZINC000680731431 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680731431 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/716 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680731431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731431 none CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 3, 10, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/717 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680731431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731431 none CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680731431 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 Building ZINC000680731431 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680731431 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 716) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680731431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731431 none CNC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 3, 10, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 717) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1) `ZINC000680731431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680731431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680731431 none CNC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000680731431 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000680731431 Building ZINC000725739281 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000725739281 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/718 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/718' -> `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)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000725739281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739281 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 13, 20, 28, 28, 28, 28, 28, 28, 37, 37, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 17, 17, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/719 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/719' -> `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)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000725739281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739281 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 10, 10, 10, 19, 24, 24, 24, 24, 24, 24, 34, 34, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 14, 14, 24, 24, 24, 24, 24, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000725739281 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 Building ZINC000725739281 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000725739281 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 718) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000725739281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739281 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 12, 13, 20, 28, 28, 28, 28, 28, 28, 37, 37, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 17, 17, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 719) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000725739281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739281 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 10, 10, 10, 19, 24, 24, 24, 24, 24, 24, 34, 34, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 14, 14, 24, 24, 24, 24, 24, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000725739281 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739281 Building ZINC000725739282 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000725739282 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/720 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/720' -> `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)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000725739282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739282 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 16, 16, 16, 24, 26, 26, 26, 26, 26, 26, 40, 40, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 6, 21, 21, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/721 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/721' -> `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)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000725739282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739282 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 13, 25, 30, 30, 30, 30, 30, 30, 40, 40, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 18, 30, 30, 30, 30, 30, 30, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000725739282 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 Building ZINC000725739282 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000725739282 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 720) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000725739282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739282 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 16, 16, 16, 24, 26, 26, 26, 26, 26, 26, 40, 40, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 6, 21, 21, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 721) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC000725739282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000725739282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000725739282 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 13, 25, 30, 30, 30, 30, 30, 30, 40, 40, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 18, 30, 30, 30, 30, 30, 30, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000725739282 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000725739282 Building ZINC000726375962 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726375962 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/722 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1) `ZINC000726375962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726375962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 6, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/723 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1) `ZINC000726375962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726375962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 8, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 4, 2, 2, 2, 13, 13, 9, 13, 2, 2, 2, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726375962 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 Building ZINC000726375962 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726375962 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 722) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1) `ZINC000726375962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726375962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 6, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 723) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1) `ZINC000726375962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726375962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375962 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 8, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 4, 2, 2, 2, 13, 13, 9, 13, 2, 2, 2, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726375962 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375962 Building ZINC000726375965 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726375965 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/724 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1) `ZINC000726375965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726375965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375965 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 5, 2, 2, 2, 13, 13, 3, 13, 2, 2, 2, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/725 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1) `ZINC000726375965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726375965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375965 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 5, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726375965 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 Building ZINC000726375965 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726375965 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 724) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1) `ZINC000726375965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726375965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375965 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 5, 2, 2, 2, 13, 13, 3, 13, 2, 2, 2, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 725) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1) `ZINC000726375965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726375965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000726375965 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2OCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 5, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726375965 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726375965 Building ZINC000726625511 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726625511 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/726 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726625511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625511 none COC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 8, 11, 11, 11, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/727 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726625511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625511 none COC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 7, 10, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 10, 10, 10, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726625511 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 Building ZINC000726625511 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726625511 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 726) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726625511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625511 none COC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 8, 11, 11, 11, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 727) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726625511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625511 none COC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 7, 10, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 10, 10, 10, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726625511 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625511 Building ZINC000726625513 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726625513 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/728 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726625513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625513 none COC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 7, 10, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 7, 10, 10, 10, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 41 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/729 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726625513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625513 none COC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 8, 11, 11, 11, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726625513 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 Building ZINC000726625513 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726625513 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 728) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726625513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625513 none COC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 7, 10, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 7, 10, 10, 10, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 41 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 729) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC000726625513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726625513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000726625513 none COC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 8, 11, 11, 11, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726625513 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726625513 Building ZINC000726765240 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726765240 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/730 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1) `ZINC000726765240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726765240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000726765240 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 10, 10, 10, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 4, 4, 4, 4, 4, 4, 2, 6, 6, 19, 41, 41, 41, 41, 6, 6, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/731 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1) `ZINC000726765240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726765240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000726765240 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 10, 10, 10, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 4, 4, 4, 4, 4, 4, 2, 6, 6, 19, 41, 41, 41, 41, 6, 6, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726765240 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 Building ZINC000726765240 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726765240 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 730) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1) `ZINC000726765240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726765240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000726765240 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 10, 10, 10, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 4, 4, 4, 4, 4, 4, 2, 6, 6, 19, 41, 41, 41, 41, 6, 6, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 731) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1) `ZINC000726765240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726765240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000726765240 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3cccc(C(F)(F)F)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 10, 10, 10, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 4, 4, 4, 4, 4, 4, 2, 6, 6, 19, 41, 41, 41, 41, 6, 6, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000726765240 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000726765240 Building ZINC000749549047 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749549047 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/732 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/732' -> `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)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC000749549047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749549047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749549047 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 12, 11, 23, 36, 36, 36, 36, 49, 49, 49, 49, 49, 49, 36, 36, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 36, 36, 36, 36, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/733 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/733' -> `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)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC000749549047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749549047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749549047 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 11, 9, 21, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 36, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 3, 3] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749549047 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 Building ZINC000749549047 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749549047 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 732) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC000749549047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749549047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749549047 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 12, 11, 23, 36, 36, 36, 36, 49, 49, 49, 49, 49, 49, 36, 36, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 36, 36, 36, 36, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 733) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC000749549047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749549047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749549047 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 11, 9, 21, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 36, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 3, 3] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749549047 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749549047 Building ZINC000749551368 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749551368 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/734 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/734' -> `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)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC000749551368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749551368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749551368 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 19, 32, 32, 32, 32, 44, 44, 44, 44, 44, 44, 32, 32, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 32, 32, 32, 32, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/735 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/735' -> `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)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC000749551368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749551368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749551368 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 11, 11, 17, 31, 31, 31, 31, 44, 44, 44, 44, 44, 44, 31, 31, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 31, 31, 31, 31, 31, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749551368 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 Building ZINC000749551368 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749551368 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 734) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC000749551368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749551368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749551368 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 19, 32, 32, 32, 32, 44, 44, 44, 44, 44, 44, 32, 32, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 32, 32, 32, 32, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 735) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC000749551368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749551368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749551368 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 11, 11, 17, 31, 31, 31, 31, 44, 44, 44, 44, 44, 44, 31, 31, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 31, 31, 31, 31, 31, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749551368 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749551368 Building ZINC000749556180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749556180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/736 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/736' -> `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)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749556180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556180 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 4, 11, 10, 12, 33, 46, 46, 46, 46, 46, 46, 49, 49, 49, 49, 49, 49, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 33, 33, 46, 46, 46, 46, 46, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/737 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/737' -> `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)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749556180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556180 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 11, 10, 12, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 31, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749556180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 Building ZINC000749556180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749556180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 736) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749556180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556180 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 4, 11, 10, 12, 33, 46, 46, 46, 46, 46, 46, 49, 49, 49, 49, 49, 49, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 33, 33, 46, 46, 46, 46, 46, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 737) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749556180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556180 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 11, 10, 12, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 31, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749556180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556180 Building ZINC000749556182 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749556182 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/738 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/738' -> `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)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749556182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556182 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 12, 11, 13, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 31, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/739 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/739' -> `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)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749556182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556182 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 11, 11, 13, 30, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 30, 30, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749556182 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 Building ZINC000749556182 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749556182 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 738) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749556182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556182 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 12, 11, 13, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 31, 31, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 739) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1) `ZINC000749556182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749556182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749556182 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 11, 11, 13, 30, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 30, 30, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749556182 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749556182 Building ZINC000749835073 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749835073 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/740 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/740' -> `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)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835073 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 9, 9, 9, 9, 9, 21, 25, 25, 25, 25, 25, 25, 35, 35, 36, 36, 36, 36, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 14, 14, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/741 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/741' -> `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)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835073 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 10, 10, 10, 10, 10, 24, 26, 26, 26, 26, 26, 26, 39, 39, 39, 39, 39, 39, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 15, 15, 26, 26, 26, 26, 26, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749835073 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 Building ZINC000749835073 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749835073 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 740) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835073 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 9, 9, 9, 9, 9, 21, 25, 25, 25, 25, 25, 25, 35, 35, 36, 36, 36, 36, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 14, 14, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 741) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835073 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 10, 10, 10, 10, 10, 24, 26, 26, 26, 26, 26, 26, 39, 39, 39, 39, 39, 39, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 15, 15, 26, 26, 26, 26, 26, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749835073 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835073 Building ZINC000749835074 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749835074 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/742 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/742' -> `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)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749835074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835074 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 11, 11, 11, 11, 11, 23, 26, 26, 26, 26, 26, 26, 38, 38, 39, 39, 39, 39, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 18, 18, 26, 26, 26, 26, 26, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/743 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/743' -> `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)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749835074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835074 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 10, 10, 10, 10, 10, 21, 25, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 15, 15, 25, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749835074 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 Building ZINC000749835074 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749835074 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 742) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749835074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835074 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 11, 11, 11, 11, 11, 23, 26, 26, 26, 26, 26, 26, 38, 38, 39, 39, 39, 39, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 18, 18, 26, 26, 26, 26, 26, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 743) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1) `ZINC000749835074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749835074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000749835074 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)OC[C@H]2CCCN2C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 10, 10, 10, 10, 10, 21, 25, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 15, 15, 25, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000749835074 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000749835074 Building ZINC000750862416 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000750862416 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/744 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1) `ZINC000750862416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000750862416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 7, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 2, 2, 2, 16, 16, 10, 16, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/745 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1) `ZINC000750862416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000750862416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 8, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 4, 4, 4, 17, 17, 8, 17, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000750862416 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 Building ZINC000750862416 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000750862416 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 744) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1) `ZINC000750862416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000750862416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 7, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 2, 2, 2, 16, 16, 10, 16, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 745) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1) `ZINC000750862416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000750862416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862416 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 8, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 4, 4, 4, 17, 17, 8, 17, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000750862416 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862416 Building ZINC000750862417 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000750862417 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/746 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1) `ZINC000750862417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000750862417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862417 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 2, 2, 2, 15, 15, 3, 15, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 71 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/747 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1) `ZINC000750862417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000750862417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862417 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 3, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 2, 2, 2, 15, 15, 3, 15, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 64 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000750862417 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 Building ZINC000750862417 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000750862417 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 746) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1) `ZINC000750862417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000750862417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862417 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 2, 2, 2, 15, 15, 3, 15, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 71 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 747) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1) `ZINC000750862417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000750862417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000750862417 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C1OCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 3, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 2, 2, 2, 15, 15, 3, 15, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 64 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000750862417 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000750862417 Building ZINC000751043235 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751043235 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/748 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1) `ZINC000751043235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751043235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000751043235 none COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 29, 30, 30, 21, 17, 5, 17, 17, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 9, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 21, 5, 2, 4, 4, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/749 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1) `ZINC000751043235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751043235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000751043235 none COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 29, 30, 30, 21, 17, 5, 17, 17, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 9, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 21, 5, 2, 4, 4, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000751043235 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 Building ZINC000751043235 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751043235 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 748) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1) `ZINC000751043235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751043235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000751043235 none COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 29, 30, 30, 21, 17, 5, 17, 17, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 9, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 21, 5, 2, 4, 4, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 749) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1) `ZINC000751043235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751043235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000751043235 none COc1ccccc1NS(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 29, 30, 30, 21, 17, 5, 17, 17, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 9, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 21, 5, 2, 4, 4, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000751043235 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751043235 Building ZINC000751169769 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751169769 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/750 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/750' -> `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)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000751169769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751169769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000751169769 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 11, 11, 14, 19, 19, 19, 19, 31, 31, 42, 42, 42, 42, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 19, 19, 19, 19, 19, 42, 42, 42, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/751 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/751' -> `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)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000751169769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751169769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000751169769 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 13, 14, 23, 23, 23, 23, 33, 33, 42, 42, 42, 42, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 23, 23, 23, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000751169769 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 Building ZINC000751169769 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751169769 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 750) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000751169769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751169769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000751169769 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 11, 11, 14, 19, 19, 19, 19, 31, 31, 42, 42, 42, 42, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 19, 19, 19, 19, 19, 42, 42, 42, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 751) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000751169769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751169769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000751169769 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 13, 14, 23, 23, 23, 23, 33, 33, 42, 42, 42, 42, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 23, 23, 23, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC000751169769 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC000751169769 Building ZINC001142278836 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278836 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/752 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2c3c(ncnc3NC(=O)[C@@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1) `ZINC001142278836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142278836 none Cc1ccc(c2c3c(ncnc3NC(=O)[C@@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 5, 12, 1, 1, 11, 5, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 10, 18, 33, 5, 5, 9, 9, 17, 8, 8, 8, 8, 8, 8, 8, 5, 2, 4, 4, 4, 10, 10, 18, 18, 33, 33, 99, 17, 17, 8, 8] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/753 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2c3c(ncnc3NC(=O)[C@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1) `ZINC001142278836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142278836 none Cc1ccc(c2c3c(ncnc3NC(=O)[C@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 5, 12, 1, 1, 11, 5, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 10, 18, 33, 5, 5, 9, 9, 17, 8, 8, 8, 8, 8, 8, 8, 5, 2, 4, 4, 4, 10, 10, 18, 18, 33, 33, 99, 17, 17, 8, 8] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142278836 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 Building ZINC001142278836 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278836 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 752) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(c2c3c(ncnc3NC(=O)[C@@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1) `ZINC001142278836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142278836 none Cc1ccc(c2c3c(ncnc3NC(=O)[C@@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 5, 12, 1, 1, 11, 5, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 10, 18, 33, 5, 5, 9, 9, 17, 8, 8, 8, 8, 8, 8, 8, 5, 2, 4, 4, 4, 10, 10, 18, 18, 33, 33, 99, 17, 17, 8, 8] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 753) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(c2c3c(ncnc3NC(=O)[C@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1) `ZINC001142278836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142278836 none Cc1ccc(c2c3c(ncnc3NC(=O)[C@]([O-])([SiH3])c3ccco3)n(CCCO)c2C(=O)CF)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 5, 12, 1, 1, 11, 5, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 10, 18, 33, 5, 5, 9, 9, 17, 8, 8, 8, 8, 8, 8, 8, 5, 2, 4, 4, 4, 10, 10, 18, 18, 33, 33, 99, 17, 17, 8, 8] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142278836 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142278836 Building ZINC001142280239 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142280239 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/754 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccco1)C2) `ZINC001142280239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142280239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142280239 none CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccco1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 28, 12, 28, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 20, 20, 20, 20, 12, 12, 12, 12, 12, 2, 1, 5, 1, 1, 1, 2, 2, 2, 2, 12, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 2, 2, 2, 12, 12] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/755 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccco1)C2) `ZINC001142280239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142280239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142280239 none CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccco1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 23, 9, 23, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 25, 26, 26, 26, 9, 9, 9, 9, 9, 3, 1, 5, 1, 1, 1, 2, 2, 2, 2, 9, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 2, 2, 2, 9, 9] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142280239 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 Building ZINC001142280239 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142280239 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 754) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccco1)C2) `ZINC001142280239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142280239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142280239 none CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccco1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 28, 12, 28, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 20, 20, 20, 20, 12, 12, 12, 12, 12, 2, 1, 5, 1, 1, 1, 2, 2, 2, 2, 12, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 2, 2, 2, 12, 12] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 755) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccco1)C2) `ZINC001142280239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142280239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142280239 none CCOC(=O)[C@@]12CCC3(CCN(C(=O)OC(C)(C)C)CC3)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccco1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 23, 9, 23, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 25, 26, 26, 26, 9, 9, 9, 9, 9, 3, 1, 5, 1, 1, 1, 2, 2, 2, 2, 9, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 2, 2, 2, 9, 9] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142280239 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142280239 Building ZINC001142282482 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282482 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/756 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@@]([O-])([SiH3])c2ccco2)s1) `ZINC001142282482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142282482 none Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@@]([O-])([SiH3])c2ccco2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 16, 6, 4, 6, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 1, 1, 1, 5, 5, 5, 5, 27, 27, 27, 27, 16, 16, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/757 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@]([O-])([SiH3])c2ccco2)s1) `ZINC001142282482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142282482 none Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@]([O-])([SiH3])c2ccco2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 16, 6, 4, 6, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 1, 1, 1, 5, 5, 5, 5, 28, 28, 28, 28, 16, 16, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282482 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 Building ZINC001142282482 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282482 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 756) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@@]([O-])([SiH3])c2ccco2)s1) `ZINC001142282482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142282482 none Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@@]([O-])([SiH3])c2ccco2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 16, 6, 4, 6, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 1, 1, 1, 5, 5, 5, 5, 27, 27, 27, 27, 16, 16, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 757) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@]([O-])([SiH3])c2ccco2)s1) `ZINC001142282482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142282482 none Cc1nnc(CN(CCN2C(=O)c3cccc4cccc(c43)C2=O)C(=O)[C@]([O-])([SiH3])c2ccco2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 16, 6, 4, 6, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 1, 1, 1, 5, 5, 5, 5, 28, 28, 28, 28, 16, 16, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282482 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282482 Building ZINC001142282517 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282517 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/758 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142282517 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 15, 15, 11, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 15, 15, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 4, 15, 15, 45, 45, 45, 45, 45, 45, 15, 15, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/759 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142282517 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 16, 16, 14, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 7, 7, 7, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 7, 7, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7] 50 rigid atoms, others: [26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282517 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 Building ZINC001142282517 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282517 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 758) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142282517 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 15, 15, 11, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 15, 15, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 4, 15, 15, 45, 45, 45, 45, 45, 45, 15, 15, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 759) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142282517 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 16, 16, 14, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 7, 7, 7, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 7, 7, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7] 50 rigid atoms, others: [26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282517 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282517 Building ZINC001142282629 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282629 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/760 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@@]([O-])([SiH3])c2ccco2)cc1) `ZINC001142282629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282629 none COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@@]([O-])([SiH3])c2ccco2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 11, 12, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 1, 1, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 41, 42, 43, 44, 45, 46, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49, 50, 51, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/761 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@]([O-])([SiH3])c2ccco2)cc1) `ZINC001142282629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282629 none COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@]([O-])([SiH3])c2ccco2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 11, 12, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 1, 1, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 41, 42, 43, 44, 45, 46, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49, 50, 51, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282629 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 Building ZINC001142282629 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282629 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 760) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@@]([O-])([SiH3])c2ccco2)cc1) `ZINC001142282629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282629 none COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@@]([O-])([SiH3])c2ccco2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 11, 12, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 1, 1, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 41, 42, 43, 44, 45, 46, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49, 50, 51, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 761) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@]([O-])([SiH3])c2ccco2)cc1) `ZINC001142282629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282629 none COC(=O)Cc1ccc(CN(Cc2ccc(CC(=O)OC)cc2)C(=O)[C@]([O-])([SiH3])c2ccco2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 5, 1, 11, 12, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 1, 1, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 41, 42, 43, 44, 45, 46, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49, 50, 51, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282629 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282629 Building ZINC001142282675 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282675 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/762 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1) `ZINC001142282675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282675 none O=C(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'H', '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', 'C.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 10, 35, 35, 42, 42, 40, 42, 42, 35, 42, 42, 40, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 105, 42, 42, 41, 42, 42, 42, 42, 41, 42, 42] 150 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/763 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1) `ZINC001142282675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282675 none O=C(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'H', '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', 'C.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 35, 35, 41, 41, 39, 41, 41, 35, 42, 42, 39, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 105, 41, 41, 40, 41, 41, 42, 42, 41, 42, 42] 150 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282675 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 Building ZINC001142282675 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282675 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 762) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1) `ZINC001142282675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282675 none O=C(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'H', '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', 'C.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 10, 35, 35, 42, 42, 40, 42, 42, 35, 42, 42, 40, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 105, 42, 42, 41, 42, 42, 42, 42, 41, 42, 42] 150 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 763) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1) `ZINC001142282675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142282675 none O=C(O[C@H]1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccco1)C(O)(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'H', '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', 'C.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 35, 35, 41, 41, 39, 41, 41, 35, 42, 42, 39, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 105, 41, 41, 40, 41, 41, 42, 42, 41, 42, 42] 150 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282675 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282675 Building ZINC001142282838 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282838 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/764 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142282838 none CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 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: [2, 1, 2, 4, 5, 5, 5, 15, 15, 9, 15, 15, 15, 5, 5, 21, 21, 21, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 5, 15, 15, 15, 15, 31, 31, 31, 31, 5, 1, 1, 1] 50 rigid atoms, others: [32, 1, 48, 49, 50, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/765 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142282838 none CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 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: [2, 1, 2, 5, 7, 7, 7, 16, 16, 11, 16, 16, 16, 7, 7, 23, 23, 23, 33, 33, 33, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 16, 16, 16, 16, 33, 33, 33, 33, 7, 1, 1, 1] 50 rigid atoms, others: [32, 1, 48, 49, 50, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282838 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 Building ZINC001142282838 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282838 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 764) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142282838 none CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 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: [2, 1, 2, 4, 5, 5, 5, 15, 15, 9, 15, 15, 15, 5, 5, 21, 21, 21, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 5, 15, 15, 15, 15, 31, 31, 31, 31, 5, 1, 1, 1] 50 rigid atoms, others: [32, 1, 48, 49, 50, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 765) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142282838 none CN(Cc1cc(c2ccccc2F)n(S(=O)(=O)c2cccnc2)c1)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 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: [2, 1, 2, 5, 7, 7, 7, 16, 16, 11, 16, 16, 16, 7, 7, 23, 23, 23, 33, 33, 33, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 16, 16, 16, 16, 33, 33, 33, 33, 7, 1, 1, 1] 50 rigid atoms, others: [32, 1, 48, 49, 50, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142282838 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142282838 Building ZINC001142283613 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283613 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/766 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)ccc32)cs1) `ZINC001142283613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142283613 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 14, 14, 46, 46, 46, 46, 46, 39, 39, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 14, 14, 46] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/767 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccco4)ccc32)cs1) `ZINC001142283613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142283613 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccco4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 14, 14, 46, 46, 46, 46, 46, 38, 38, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 13, 14, 46] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142283613 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 Building ZINC001142283613 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283613 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 766) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)ccc32)cs1) `ZINC001142283613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142283613 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 14, 14, 46, 46, 46, 46, 46, 39, 39, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 14, 14, 46] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 767) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccco4)ccc32)cs1) `ZINC001142283613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142283613 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccco4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 14, 14, 46, 46, 46, 46, 46, 38, 38, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 13, 14, 46] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142283613 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142283613 Building ZINC001142284180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/768 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1)c1ccccn1) `ZINC001142284180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142284180 none CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1)c1ccccn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 18, 49, 18, 10, 10, 6, 10, 6, 6, 6, 6, 6, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 18, 18, 18, 18, 6, 6, 7, 7, 7, 7, 2, 5, 5, 5, 6, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/769 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1)c1ccccn1) `ZINC001142284180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142284180 none CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1)c1ccccn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 17, 47, 17, 9, 9, 6, 9, 6, 6, 6, 6, 6, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 17, 17, 17, 17, 6, 6, 7, 7, 7, 7, 2, 5, 5, 5, 6, 9, 9, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142284180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 Building ZINC001142284180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 768) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1)c1ccccn1) `ZINC001142284180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142284180 none CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1)c1ccccn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 18, 49, 18, 10, 10, 6, 10, 6, 6, 6, 6, 6, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 18, 18, 18, 18, 6, 6, 7, 7, 7, 7, 2, 5, 5, 5, 6, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 769) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1)c1ccccn1) `ZINC001142284180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142284180 none CCOC(=O)CCN(C(=O)c1ccc(NC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1)c1ccccn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 17, 47, 17, 9, 9, 6, 9, 6, 6, 6, 6, 6, 7, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 17, 17, 17, 17, 6, 6, 7, 7, 7, 7, 2, 5, 5, 5, 6, 9, 9, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142284180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142284180 Building ZINC001142286086 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286086 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/770 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1N=C(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3) `ZINC001142286086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142286086 none CC(=O)N1N=C(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 12, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 22, 10, 14, 14, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 14, 14, 4, 8, 8, 8, 14, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/771 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1N=C(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3) `ZINC001142286086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142286086 none CC(=O)N1N=C(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 12, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 5, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 3, 8, 8, 8, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142286086 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 Building ZINC001142286086 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286086 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 770) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1N=C(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3) `ZINC001142286086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142286086 none CC(=O)N1N=C(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 12, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 22, 10, 14, 14, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 14, 14, 4, 8, 8, 8, 14, 14, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 771) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1N=C(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3) `ZINC001142286086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142286086 none CC(=O)N1N=C(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccco3)cc2)c2cc3c(cc2C[C@H]1C)OCO3 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 12, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 5, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 3, 8, 8, 8, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142286086 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286086 Building ZINC001142286410 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286410 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/772 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286410 none Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 50, 50, 49, 49, 49, 49, 49, 31, 10, 10, 4, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 49, 31, 31, 9, 10, 10, 3, 4, 4, 4, 10] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/773 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286410 none Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 46, 46, 46, 46, 30, 9, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 46, 30, 30, 2, 9, 9, 2, 4, 4, 4, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142286410 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 Building ZINC001142286410 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286410 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 772) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286410 none Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 50, 50, 49, 49, 49, 49, 49, 31, 10, 10, 4, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 49, 31, 31, 9, 10, 10, 3, 4, 4, 4, 10] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 773) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286410 none Cn1c2cc([S@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 46, 46, 46, 46, 30, 9, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 46, 30, 30, 2, 9, 9, 2, 4, 4, 4, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142286410 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286410 Building ZINC001142286411 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286411 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/774 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286411 none Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 46, 46, 46, 46, 30, 9, 9, 3, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 46, 30, 30, 8, 9, 9, 2, 4, 4, 4, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/775 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286411 none Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 50, 50, 49, 49, 49, 49, 49, 31, 10, 10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 10, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 49, 31, 31, 3, 10, 10, 3, 3, 3, 3, 10] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142286411 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 Building ZINC001142286411 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286411 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 774) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286411 none Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 46, 46, 46, 46, 30, 9, 9, 3, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 46, 30, 30, 8, 9, 9, 2, 4, 4, 4, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 775) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21) `ZINC001142286411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142286411 none Cn1c2cc([S@@](C)=O)sc2c2cnn(Cc3cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c3)c(=O)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.2', '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, 8, 1, 1, 1, 14, 5, 11, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 50, 50, 49, 49, 49, 49, 49, 31, 10, 10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 10, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 49, 31, 31, 3, 10, 10, 3, 3, 3, 3, 10] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142286411 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142286411 Building ZINC001142287185 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287185 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/776 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C(=O)N12) `ZINC001142287185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142287185 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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: [24, 9, 24, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 9, 9, 9, 3, 7, 7, 7] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/777 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C(=O)N12) `ZINC001142287185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142287185 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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: [22, 6, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 4, 4, 4] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142287185 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 Building ZINC001142287185 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287185 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 776) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C(=O)N12) `ZINC001142287185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142287185 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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: [24, 9, 24, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 9, 9, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 9, 9, 9, 3, 7, 7, 7] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 777) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C(=O)N12) `ZINC001142287185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142287185 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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: [22, 6, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 4, 4, 4] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142287185 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142287185 Building ZINC001142288173 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288173 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/778 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(C)C) `ZINC001142288173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001142288173 none CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 31, 50, 50, 50, 50, 50, 50, 16, 16, 8, 8, 5, 8, 2, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 8, 2, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 234 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/779 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(C)C) `ZINC001142288173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001142288173 none CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 8, 13, 13, 6, 8, 8, 15, 15, 24, 50, 50, 50, 50, 50, 50, 15, 16, 6, 6, 6, 6, 3, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 6, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 6, 6, 6, 3, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 252 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142288173 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 Building ZINC001142288173 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288173 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 778) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(C)C) `ZINC001142288173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001142288173 none CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 31, 50, 50, 50, 50, 50, 50, 16, 16, 8, 8, 5, 8, 2, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 8, 2, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 234 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 779) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(C)C) `ZINC001142288173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001142288173 none CC[C@H](C)[C@@H]([C@@H](CC(=O)OC(C)(C)C)OC)N(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 8, 5, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 8, 13, 13, 6, 8, 8, 15, 15, 24, 50, 50, 50, 50, 50, 50, 15, 16, 6, 6, 6, 6, 3, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 6, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 6, 6, 6, 3, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 252 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142288173 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142288173 Building ZINC001142685745 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685745 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/780 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685745 none O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 18, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 16, 22, 39, 49, 49, 12, 12, 7, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 20, 20, 20, 12, 12, 12, 12, 16, 16, 39, 39, 49, 49, 49, 49, 49, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/781 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685745 none O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 19, 24, 42, 49, 49, 14, 14, 9, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 23, 23, 23, 14, 14, 14, 14, 19, 19, 42, 42, 49, 49, 49, 49, 49, 14, 14, 14, 14, 1, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685745 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 Building ZINC001142685745 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685745 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 780) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685745 none O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 18, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 16, 22, 39, 49, 49, 12, 12, 7, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 20, 20, 20, 12, 12, 12, 12, 16, 16, 39, 39, 49, 49, 49, 49, 49, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 781) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685745 none O=C(c1ccco1)N1CC2(C[C@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 19, 24, 42, 49, 49, 14, 14, 9, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 23, 23, 23, 14, 14, 14, 14, 19, 19, 42, 42, 49, 49, 49, 49, 49, 14, 14, 14, 14, 1, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685745 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685745 Building ZINC001142685746 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685746 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/782 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685746 none O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 16, 24, 43, 48, 48, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 10, 10, 10, 10, 16, 16, 43, 43, 48, 48, 48, 48, 48, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/783 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685746 none O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 16, 26, 44, 49, 49, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 10, 10, 10, 10, 16, 16, 44, 44, 49, 49, 49, 49, 49, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685746 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 Building ZINC001142685746 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685746 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 782) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685746 none O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 16, 24, 43, 48, 48, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 10, 10, 10, 10, 16, 16, 43, 43, 48, 48, 48, 48, 48, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 783) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2) `ZINC001142685746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142685746 none O=C(c1ccco1)N1CC2(C[C@@H]1COCC1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 16, 26, 44, 49, 49, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 10, 10, 10, 10, 16, 16, 44, 44, 49, 49, 49, 49, 49, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [54, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685746 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685746 Building ZINC001142685919 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685919 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/784 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685919 none CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 25, 50, 11, 11, 11, 11, 11, 11, 9, 6, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 175 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/785 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685919 none CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 22, 49, 9, 9, 9, 9, 9, 9, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 173 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685919 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 Building ZINC001142685919 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685919 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 784) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685919 none CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 25, 50, 11, 11, 11, 11, 11, 11, 9, 6, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 175 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 785) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685919 none CN1CCN(C(=O)C[C@@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 22, 49, 9, 9, 9, 9, 9, 9, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 173 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685919 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685919 Building ZINC001142685920 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685920 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/786 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685920 none CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 28, 46, 10, 10, 10, 10, 10, 10, 8, 4, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/787 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685920 none CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 26, 44, 8, 8, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685920 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 Building ZINC001142685920 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685920 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 786) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685920 none CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 28, 46, 10, 10, 10, 10, 10, 10, 8, 4, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 787) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1) `ZINC001142685920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001142685920 none CN1CCN(C(=O)C[C@H]2CC3(CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 26, 44, 8, 8, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 50, 15, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142685920 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142685920 Building ZINC001142686085 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686085 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/788 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCN1[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O) `ZINC001142686085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142686085 none CC(C)CCN1[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 22, 1, 21, 1, 1, 1, 2, 2, 1, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 2, 2, 1, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 156 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/789 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCN1[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O) `ZINC001142686085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142686085 none CC(C)CCN1[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 19, 1, 17, 1, 1, 1, 2, 2, 1, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 2, 2, 1, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142686085 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 Building ZINC001142686085 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686085 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 788) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)CCN1[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O) `ZINC001142686085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142686085 none CC(C)CCN1[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 22, 1, 21, 1, 1, 1, 2, 2, 1, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 2, 2, 1, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 156 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 789) grep: /scratch/xiaobo/236261/xbz-8058088.52/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)CCN1[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O) `ZINC001142686085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001142686085 none CC(C)CCN1[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC[C@@H]2Oc2ccccc2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 19, 1, 17, 1, 1, 1, 2, 2, 1, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 2, 2, 1, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142686085 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686085 Building ZINC001142686367 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686367 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/790 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142686367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC001142686367 none CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 7, 7, 7, 6, 1, 1, 1, 2, 2, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 4, 4, 2, 2, 2, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [64, 65, 66, 67, 68, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 69, 70, 71, 72]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/791 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142686367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC001142686367 none CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 14, 7, 14, 7, 7, 7, 6, 2, 2, 2, 3, 3, 5, 7, 7, 7, 7, 7, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 5, 5, 3, 3, 3, 3, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [64, 65, 66, 67, 68, 22, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 69, 70, 71, 72]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142686367 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 Building ZINC001142686367 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686367 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 790) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142686367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC001142686367 none CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 7, 7, 7, 6, 1, 1, 1, 2, 2, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 4, 4, 2, 2, 2, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [64, 65, 66, 67, 68, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 69, 70, 71, 72]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 791) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142686367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 76 natoms 75 natoms 74 natoms 73 names: ZINC001142686367 none CC(C)(C)OC(=O)N1CCC(CN(CCCN2CCOCC2)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 14, 7, 14, 7, 7, 7, 6, 2, 2, 2, 3, 3, 5, 7, 7, 7, 7, 7, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 5, 5, 3, 3, 3, 3, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [64, 65, 66, 67, 68, 22, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 69, 70, 71, 72]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142686367 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142686367 Building ZINC001142687073 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687073 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/792 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687073 none CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 46, 41, 18, 8, 7, 8, 8, 4, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 18, 18, 8, 8, 3, 3, 6, 2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [64, 65, 63, 62, 61, 17, 18, 19, 20, 21, 22, 23, 59, 60, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 66, 67]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/793 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687073 none CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 48, 45, 21, 3, 3, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 21, 21, 8, 8, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 66, 67]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142687073 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 Building ZINC001142687073 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687073 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 792) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687073 none CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 46, 41, 18, 8, 7, 8, 8, 4, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 18, 18, 8, 8, 3, 3, 6, 2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [64, 65, 63, 62, 61, 17, 18, 19, 20, 21, 22, 23, 59, 60, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 66, 67]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 793) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687073 none CC(C)OCCOCc1ccc(OC[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 48, 45, 21, 3, 3, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 21, 21, 8, 8, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 66, 67]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142687073 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687073 Building ZINC001142687074 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687074 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/794 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687074 none CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 48, 44, 22, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 22, 22, 7, 7, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 66, 67]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/795 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687074 none CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 45, 40, 18, 4, 4, 8, 8, 4, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 18, 18, 8, 8, 3, 3, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 66, 67]) total number of confs: 170 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142687074 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 Building ZINC001142687074 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687074 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 794) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687074 none CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 48, 44, 22, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 22, 22, 7, 7, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 66, 67]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 795) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1) `ZINC001142687074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142687074 none CC(C)OCCOCc1ccc(OC[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 45, 40, 18, 4, 4, 8, 8, 4, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 18, 18, 8, 8, 3, 3, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 66, 67]) total number of confs: 170 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142687074 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687074 Building ZINC001142687621 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687621 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/796 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142687621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142687621 none CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 3, 3, 3, 3, 2, 3, 4, 5, 16, 16, 16, 28, 28, 27, 28, 28, 28, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 4, 4, 5, 5, 16, 28, 28, 27, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [59, 60, 56, 58, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 61, 62, 63, 64]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/797 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142687621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142687621 none CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 9, 3, 9, 3, 3, 3, 3, 2, 3, 5, 6, 16, 16, 16, 29, 29, 28, 29, 29, 29, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 5, 5, 6, 6, 16, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [59, 60, 56, 58, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 61, 62, 63, 64]) total number of confs: 139 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142687621 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 Building ZINC001142687621 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687621 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 796) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142687621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142687621 none CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 3, 3, 3, 3, 2, 3, 4, 5, 16, 16, 16, 28, 28, 27, 28, 28, 28, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 4, 4, 5, 5, 16, 28, 28, 27, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [59, 60, 56, 58, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 61, 62, 63, 64]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 797) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC001142687621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142687621 none CCOC(=O)N1CCC(N(CCNC(=O)c2ccccc2C)C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 9, 3, 9, 3, 3, 3, 3, 2, 3, 5, 6, 16, 16, 16, 29, 29, 28, 29, 29, 29, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 5, 5, 6, 6, 16, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [59, 60, 56, 58, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 61, 62, 63, 64]) total number of confs: 139 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142687621 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142687621 Building ZINC001142688179 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142688179 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/798 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 36, 36, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/799 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 38, 38, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/800 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/800' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 24, 15, 15, 15, 15, 8, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 39, 39, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/801 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/801' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 14, 14, 14, 14, 8, 14, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 38, 38, 24, 24, 14, 14, 14, 14, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142688179 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 Building ZINC001142688179 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142688179 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 798) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 36, 36, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 799) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 38, 38, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 800) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 24, 15, 15, 15, 15, 8, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 39, 39, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 801) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 14, 14, 14, 14, 8, 14, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 38, 38, 24, 24, 14, 14, 14, 14, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142688179 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 Building ZINC001142688179 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142688179 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 798) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 36, 36, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 799) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 38, 38, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 800) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 24, 15, 15, 15, 15, 8, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 39, 39, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 801) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 14, 14, 14, 14, 8, 14, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 38, 38, 24, 24, 14, 14, 14, 14, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142688179 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 Building ZINC001142688179 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142688179 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 798) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 36, 36, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 799) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 15, 15, 15, 15, 7, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 38, 38, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 800) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 24, 15, 15, 15, 15, 8, 15, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 39, 39, 24, 24, 15, 15, 15, 15, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 801) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1) `ZINC001142688179.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142688179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001142688179 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 24, 14, 14, 14, 14, 8, 14, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 38, 38, 24, 24, 14, 14, 14, 14, 4, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [22, 19, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142688179 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688179 Building ZINC001142688388 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688388 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/802 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142688388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142688388 none CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 36, 9, 9, 4, 9, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 4, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 36, 36, 9, 4, 2, 2, 2, 1, 2, 2, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 210 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/803 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142688388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142688388 none CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 36, 10, 10, 4, 10, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 4, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 36, 36, 10, 4, 2, 2, 2, 1, 2, 2, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 206 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142688388 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 Building ZINC001142688388 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688388 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 802) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142688388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142688388 none CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 36, 9, 9, 4, 9, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 4, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 36, 36, 9, 4, 2, 2, 2, 1, 2, 2, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 210 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 803) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142688388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142688388 none CCN(CC)CCNC(=O)c1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 36, 10, 10, 4, 10, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 4, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 36, 36, 10, 4, 2, 2, 2, 1, 2, 2, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 206 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142688388 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142688388 Building ZINC001142691659 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691659 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/804 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 13, 30, 30, 35, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 6, 13, 13, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 4, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/805 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/806 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/806' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/807 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/807' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 30, 30, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691659 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 Building ZINC001142691659 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691659 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 804) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 13, 30, 30, 35, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 6, 13, 13, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 4, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 805) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 806) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 807) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 30, 30, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691659 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 Building ZINC001142691659 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691659 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 804) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 13, 30, 30, 35, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 6, 13, 13, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 4, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 805) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 806) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 807) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 30, 30, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691659 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 Building ZINC001142691659 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691659 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 804) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 13, 30, 30, 35, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 6, 13, 13, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 4, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 805) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 806) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 29, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 807) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691659.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142691659 none N=C(CC(=O)O[C@H]1C[N@@](C(c2ccccc2)c2ccccc2)C1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 12, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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: [4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 30, 30, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691659 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691659 Building ZINC001142691726 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691726 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/808 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C(=O)N12) `ZINC001142691726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142691726 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [20, 6, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 3, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/809 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C(=O)N12) `ZINC001142691726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142691726 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [22, 7, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 3, 7, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691726 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 Building ZINC001142691726 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691726 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 808) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C(=O)N12) `ZINC001142691726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142691726 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [20, 6, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 3, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 809) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C(=O)N12) `ZINC001142691726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001142691726 none O=C(OC(c1ccccc1)c1ccccc1)C1=CCS[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C(=O)N12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [22, 7, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 3, 7, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691726 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691726 Building ZINC001142691791 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691791 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/810 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691791 none COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 15, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 46, 46, 46, 46, 15, 21, 21, 21, 15, 15, 3, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 46, 46, 46, 46, 46, 46, 46, 46, 46, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/811 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691791 none COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 9, 16, 16, 16, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 46, 46, 46, 46, 16, 21, 21, 21, 16, 16, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691791 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 Building ZINC001142691791 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691791 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 810) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691791 none COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 15, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 46, 46, 46, 46, 15, 21, 21, 21, 15, 15, 3, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 46, 46, 46, 46, 46, 46, 46, 46, 46, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 811) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691791 none COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 9, 16, 16, 16, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 46, 46, 46, 46, 16, 21, 21, 21, 16, 16, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691791 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691791 Building ZINC001142691792 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691792 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/812 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691792 none COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 9, 16, 16, 16, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 47, 47, 47, 47, 16, 21, 21, 21, 16, 16, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 47, 47, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/813 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691792 none COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 15, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 46, 46, 46, 46, 15, 21, 21, 21, 15, 15, 3, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 46, 46, 46, 46, 46, 46, 46, 46, 46, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691792 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 Building ZINC001142691792 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691792 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 812) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691792 none COc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 9, 16, 16, 16, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 47, 47, 47, 47, 16, 21, 21, 21, 16, 16, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 47, 47, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 813) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1) `ZINC001142691792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142691792 none COc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccccc1)NC(=O)[C@]21CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 15, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 46, 46, 46, 46, 15, 21, 21, 21, 15, 15, 3, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 46, 46, 46, 46, 46, 46, 46, 46, 46, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142691792 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142691792 Building ZINC001142692141 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142692141 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/814 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142692141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142692141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142692141 none COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 11, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 29, 4, 16, 16, 31, 32, 32, 32, 31, 31, 32, 32, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 31, 31, 32, 64, 32, 4, 3, 3, 1, 3, 3] 100 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/815 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142692141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142692141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142692141 none COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 11, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 13, 25, 4, 13, 13, 28, 32, 32, 32, 28, 28, 32, 32, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 25, 25, 25, 28, 28, 32, 64, 32, 4, 3, 3, 1, 3, 3] 100 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142692141 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 Building ZINC001142692141 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142692141 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 814) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142692141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142692141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142692141 none COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 11, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 29, 4, 16, 16, 31, 32, 32, 32, 31, 31, 32, 32, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 31, 31, 32, 64, 32, 4, 3, 3, 1, 3, 3] 100 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 815) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142692141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142692141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142692141 none COC(=O)[C@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 11, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 13, 25, 4, 13, 13, 28, 32, 32, 32, 28, 28, 32, 32, 32, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 25, 25, 25, 28, 28, 32, 64, 32, 4, 3, 3, 1, 3, 3] 100 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142692141 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142692141 Building ZINC001142694151 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142694151 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/816 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@@]([O-])([SiH3])c3ccccc3)ccc12) `ZINC001142694151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142694151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142694151 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@@]([O-])([SiH3])c3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 40, 40, 40, 40, 40, 40, 13, 13, 5, 13, 3, 5, 5, 12, 13, 13, 13, 13, 13, 13, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 13, 12, 12, 13, 13, 26, 13, 13, 3, 2, 2, 1, 2, 2, 40, 40] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/817 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@]([O-])([SiH3])c3ccccc3)ccc12) `ZINC001142694151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142694151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142694151 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@]([O-])([SiH3])c3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 7, 12, 3, 7, 7, 12, 13, 13, 12, 13, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 12, 13, 13, 26, 13, 13, 3, 3, 3, 1, 3, 3, 37, 37] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142694151 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 Building ZINC001142694151 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142694151 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 816) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@@]([O-])([SiH3])c3ccccc3)ccc12) `ZINC001142694151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142694151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142694151 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@@]([O-])([SiH3])c3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 40, 40, 40, 40, 40, 40, 13, 13, 5, 13, 3, 5, 5, 12, 13, 13, 13, 13, 13, 13, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 13, 12, 12, 13, 13, 26, 13, 13, 3, 2, 2, 1, 2, 2, 40, 40] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 817) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@]([O-])([SiH3])c3ccccc3)ccc12) `ZINC001142694151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142694151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142694151 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@]([O-])([SiH3])c3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 7, 12, 3, 7, 7, 12, 13, 13, 12, 13, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 12, 13, 13, 26, 13, 13, 3, 3, 3, 1, 3, 3, 37, 37] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142694151 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142694151 Building ZINC001142695398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/818 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695398 none CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 50, 16, 16, 8, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 16, 16, 16, 8, 8, 5, 5, 3, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 171 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/819 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695398 none CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 16, 9, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 16, 16, 16, 9, 9, 6, 6, 3, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 175 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 Building ZINC001142695398 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695398 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 818) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695398 none CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 50, 16, 16, 8, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 16, 16, 16, 8, 8, 5, 5, 3, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 171 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 819) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695398 none CC(C)[C@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 16, 9, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 16, 16, 16, 9, 9, 6, 6, 3, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 175 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695398 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695398 Building ZINC001142695399 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695399 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/820 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695399 none CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 11, 7, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 11, 11, 11, 7, 7, 3, 3, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 176 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/821 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695399 none CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 12, 11, 7, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 11, 11, 11, 7, 7, 3, 3, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 177 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695399 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 Building ZINC001142695399 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695399 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 820) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695399 none CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 11, 7, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 11, 11, 11, 7, 7, 3, 3, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 176 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 821) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695399 none CC(C)[C@@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 12, 11, 7, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 11, 11, 11, 7, 7, 3, 3, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 177 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695399 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695399 Building ZINC001142695400 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695400 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/822 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695400 none CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 50, 17, 13, 7, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 13, 13, 13, 7, 7, 3, 3, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 180 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/823 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695400 none CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 50, 18, 13, 8, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 13, 13, 13, 8, 8, 4, 4, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 170 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695400 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 Building ZINC001142695400 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695400 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 822) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695400 none CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 50, 17, 13, 7, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 13, 13, 13, 7, 7, 3, 3, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 180 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 823) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695400 none CC(C)[C@@]1(C)CCO[P@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 50, 18, 13, 8, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 13, 13, 13, 8, 8, 4, 4, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 170 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695400 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695400 Building ZINC001142695401 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695401 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/824 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695401 none CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 39, 50, 22, 18, 10, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 18, 18, 18, 10, 10, 5, 5, 3, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 184 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/825 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695401 none CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 36, 50, 18, 15, 9, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 15, 15, 15, 9, 9, 4, 4, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 183 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695401 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 Building ZINC001142695401 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695401 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 824) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1) `ZINC001142695401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695401 none CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 39, 50, 22, 18, 10, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 18, 18, 18, 10, 10, 5, 5, 3, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 184 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 825) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1) `ZINC001142695401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142695401 none CC(C)[C@]1(C)CCO[P@@](=O)(CO[C@H](C)Cn2cnc3c2ncnc3NC(=O)[C@](C)([O-])[SiH3])OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 13, 11, 5, 12, 5, 7, 5, 5, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 36, 50, 18, 15, 9, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 15, 15, 15, 9, 9, 4, 4, 2, 1, 1, 1, 50, 50] 50 rigid atoms, others: [29, 57, 26, 59, 28, 58, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 60, 61]) total number of confs: 183 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142695401 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142695401 Building ZINC001142697816 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697816 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/826 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@@](C)([O-])[SiH3])CC3)s2)o1) `ZINC001142697816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142697816 none CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@@](C)([O-])[SiH3])CC3)s2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 5, 14, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 50, 51, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/827 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@](C)([O-])[SiH3])CC3)s2)o1) `ZINC001142697816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142697816 none CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@](C)([O-])[SiH3])CC3)s2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 5, 14, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [49, 50, 51, 20, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142697816 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 Building ZINC001142697816 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697816 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 826) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@@](C)([O-])[SiH3])CC3)s2)o1) `ZINC001142697816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142697816 none CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@@](C)([O-])[SiH3])CC3)s2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 5, 14, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 50, 51, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 827) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@](C)([O-])[SiH3])CC3)s2)o1) `ZINC001142697816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142697816 none CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCN(C(=O)[C@](C)([O-])[SiH3])CC3)s2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 5, 14, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [49, 50, 51, 20, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142697816 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142697816 Building ZINC001142698304 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698304 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/828 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C2)cc1) `ZINC001142698304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 4 30 3 34 to be deleted 35 to be deleted 36 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001142698304 none CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 30, 35, 37, 16, 16, 16, 16, 9, 6, 9, 3, 6, 7, 7, 12, 12, 12, 12, 12, 12, 14, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 30, 30, 16, 16, 7, 7, 7, 7, 12, 12, 12, 12, 14, 14, 14, 3, 3, 3, 3, 1, 1, 1, 3, 3, 16, 16] 50 rigid atoms, others: [32, 65, 66, 67, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 68, 69, 70, 71]) total number of confs: 176 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/829 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C2)cc1) `ZINC001142698304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 4 30 3 34 to be deleted 35 to be deleted 36 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001142698304 none CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 27, 32, 34, 14, 14, 14, 14, 9, 6, 9, 3, 6, 7, 7, 13, 13, 13, 13, 13, 13, 15, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 27, 14, 14, 7, 7, 7, 7, 13, 13, 13, 13, 15, 15, 15, 3, 3, 3, 3, 1, 1, 1, 3, 3, 14, 14] 50 rigid atoms, others: [32, 65, 66, 67, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 68, 69, 70, 71]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142698304 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 Building ZINC001142698304 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698304 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 828) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C2)cc1) `ZINC001142698304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 4 30 3 34 to be deleted 35 to be deleted 36 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001142698304 none CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 30, 35, 37, 16, 16, 16, 16, 9, 6, 9, 3, 6, 7, 7, 12, 12, 12, 12, 12, 12, 14, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 30, 30, 16, 16, 7, 7, 7, 7, 12, 12, 12, 12, 14, 14, 14, 3, 3, 3, 3, 1, 1, 1, 3, 3, 16, 16] 50 rigid atoms, others: [32, 65, 66, 67, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 68, 69, 70, 71]) total number of confs: 176 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 829) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C2)cc1) `ZINC001142698304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 4 30 3 34 to be deleted 35 to be deleted 36 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001142698304 none CCN(CC)Cc1ccc(C(=O)N(CCc2ccccc2OC)[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 27, 32, 34, 14, 14, 14, 14, 9, 6, 9, 3, 6, 7, 7, 13, 13, 13, 13, 13, 13, 15, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 27, 14, 14, 7, 7, 7, 7, 13, 13, 13, 13, 15, 15, 15, 3, 3, 3, 3, 1, 1, 1, 3, 3, 14, 14] 50 rigid atoms, others: [32, 65, 66, 67, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 68, 69, 70, 71]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142698304 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142698304 Building ZINC001142699620 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699620 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/830 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1) `ZINC001142699620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142699620 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 10, 10, 10, 10, 18, 32, 32, 32, 42, 42, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 6, 6, 6, 8, 10, 10, 18, 18, 32, 42, 42, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 34, 35, 36, 2, 3] set([4, 5, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/831 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1) `ZINC001142699620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142699620 none C[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 6, 6, 5, 6, 6, 6, 6, 8, 8, 8, 10, 10, 10, 10, 17, 31, 31, 31, 41, 41, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 6, 6, 6, 8, 10, 10, 17, 17, 31, 41, 41, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 34, 35, 36, 2, 3] set([4, 5, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142699620 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 Building ZINC001142699620 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699620 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 830) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1) `ZINC001142699620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142699620 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 10, 10, 10, 10, 18, 32, 32, 32, 42, 42, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 6, 6, 6, 8, 10, 10, 18, 18, 32, 42, 42, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 34, 35, 36, 2, 3] set([4, 5, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 831) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1) `ZINC001142699620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142699620 none C[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1NC(=O)c1ccc(CNC(=O)/C=C/c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 6, 6, 5, 6, 6, 6, 6, 8, 8, 8, 10, 10, 10, 10, 17, 31, 31, 31, 41, 41, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 6, 6, 6, 8, 10, 10, 17, 17, 31, 41, 41, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 34, 35, 36, 2, 3] set([4, 5, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142699620 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699620 Building ZINC001142699909 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699909 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/832 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1) `ZINC001142699909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142699909 none C[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 12, 12, 12, 12, 12, 12, 2, 2, 2, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 1, 1, 1, 2, 2, 2, 2, 7, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 3] set([4, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 47 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/833 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1) `ZINC001142699909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142699909 none C[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13, 2, 2, 2, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 5, 1, 1, 1, 2, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 2, 2, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 3] set([4, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 50 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142699909 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 Building ZINC001142699909 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699909 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 832) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1) `ZINC001142699909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142699909 none C[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 12, 12, 12, 12, 12, 12, 2, 2, 2, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 1, 1, 1, 2, 2, 2, 2, 7, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 3] set([4, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 47 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 833) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: C[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1) `ZINC001142699909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142699909 none C[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C(=O)Nc2ccccc2N)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13, 2, 2, 2, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 5, 1, 1, 1, 2, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 2, 2, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 3] set([4, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 50 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142699909 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142699909 Building ZINC001142702756 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142702756 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/834 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/835 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/836 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/836' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/837 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/837' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142702756 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 Building ZINC001142702756 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142702756 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 834) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 835) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 836) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 837) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142702756 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 Building ZINC001142702756 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142702756 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 834) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 835) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 836) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 837) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142702756 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 Building ZINC001142702756 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142702756 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 834) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 835) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 49, 28, 28, 28, 22, 28, 15, 5, 15, 3, 5, 3, 1, 3, 1, 1, 1, 5, 11, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 28, 28, 49, 49, 49, 28, 28, 3, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 197 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 836) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 837) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2) `ZINC001142702756.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142702756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 4 23 3 27 to be deleted 28 to be deleted 29 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142702756 none COc1cc2c(cc1OC)[C@H]1C[C@@H](OC(=O)[C@@H](NC(=O)[C@](C)([O-])[SiH3])C(C)C)[C@H](CC(C)C)CN1CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', '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, 12, 5, 5, 7, 5, 5, 7, 12, 1, 11, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 25, 19, 25, 14, 7, 14, 3, 7, 3, 1, 3, 1, 1, 1, 7, 12, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 48, 48, 48, 25, 25, 49, 49, 49, 25, 25, 3, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [50, 51, 52, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74]) total number of confs: 205 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142702756 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142702756 Building ZINC001142703136 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703136 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/838 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1) `ZINC001142703136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142703136 none C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 1, 1, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 6, 6, 6, 6, 6, 6, 5, 8, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 21, 21, 21, 39, 50, 50, 50, 50, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 30, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40] set([4, 5, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 248 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/839 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1) `ZINC001142703136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142703136 none C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 1, 1, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 11, 11, 11, 17, 17, 18, 18, 18, 18, 18, 18, 17, 18, 22, 22, 22, 37, 50, 50, 50, 50, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 9, 9, 33, 18, 18, 18, 18, 18, 18, 18, 18, 37, 37, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40] set([4, 5, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 243 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142703136 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 Building ZINC001142703136 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703136 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 838) grep: /scratch/xiaobo/236261/xbz-8058088.52/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@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1) `ZINC001142703136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142703136 none C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 1, 1, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 6, 6, 6, 6, 6, 6, 5, 8, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 21, 21, 21, 39, 50, 50, 50, 50, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 30, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40] set([4, 5, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 248 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 839) grep: /scratch/xiaobo/236261/xbz-8058088.52/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@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1) `ZINC001142703136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142703136 none C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1cncs1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 1, 1, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 11, 11, 11, 17, 17, 18, 18, 18, 18, 18, 18, 17, 18, 22, 22, 22, 37, 50, 50, 50, 50, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 9, 9, 33, 18, 18, 18, 18, 18, 18, 18, 18, 37, 37, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40] set([4, 5, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 243 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142703136 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703136 Building ZINC001142703278 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703278 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/840 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl) `ZINC001142703278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 4 19 3 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142703278 none Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'O.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 15, 1, 12, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 21, 21, 21, 12, 12, 12, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 7, 11, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 29, 29, 29, 29, 21, 12, 5, 5, 2, 1, 1, 1, 11, 11, 20, 20, 20] 50 rigid atoms, others: [43, 44, 45, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/841 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl) `ZINC001142703278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 4 19 3 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142703278 none Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'O.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 15, 1, 12, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 23, 23, 23, 14, 14, 14, 9, 7, 9, 4, 4, 1, 4, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 23, 23, 23, 30, 30, 30, 30, 23, 14, 7, 7, 4, 1, 1, 1, 12, 12, 19, 19, 19] 50 rigid atoms, others: [43, 44, 45, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142703278 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 Building ZINC001142703278 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703278 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 840) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl) `ZINC001142703278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 4 19 3 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142703278 none Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'O.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 15, 1, 12, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 21, 21, 21, 12, 12, 12, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 7, 11, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 29, 29, 29, 29, 21, 12, 5, 5, 2, 1, 1, 1, 11, 11, 20, 20, 20] 50 rigid atoms, others: [43, 44, 45, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 841) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl) `ZINC001142703278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 4 19 3 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142703278 none Cn1ncc(Cl)c1c1cc(C(=O)N[C@H](CNC(=O)[C@@](C)([O-])[SiH3])Cc2ccc(F)c(F)c2)oc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'O.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 15, 1, 12, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 23, 23, 23, 14, 14, 14, 9, 7, 9, 4, 4, 1, 4, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 23, 23, 23, 30, 30, 30, 30, 23, 14, 7, 7, 4, 1, 1, 1, 12, 12, 19, 19, 19] 50 rigid atoms, others: [43, 44, 45, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001142703278 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001142703278 Building ZINC001149767299 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149767299 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/842 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149767299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767299 none COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 27, 27, 26, 27, 27, 27, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 15, 15, 15, 27, 27, 27, 27, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/843 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149767299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767299 none COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 19, 20, 12, 19, 19, 30, 30, 30, 30, 30, 30, 12, 12, 12, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 20, 20, 20, 30, 30, 30, 30, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001149767299 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 Building ZINC001149767299 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149767299 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 842) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149767299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767299 none COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 27, 27, 26, 27, 27, 27, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 15, 15, 15, 27, 27, 27, 27, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 843) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149767299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767299 none COC(=O)[C@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 19, 20, 12, 19, 19, 30, 30, 30, 30, 30, 30, 12, 12, 12, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 20, 20, 20, 30, 30, 30, 30, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001149767299 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767299 Building ZINC001149767300 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149767300 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/844 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149767300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767300 none COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 16, 17, 8, 16, 16, 28, 28, 28, 28, 28, 28, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 17, 17, 17, 28, 28, 28, 28, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/845 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149767300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767300 none COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 11, 18, 18, 27, 27, 27, 27, 27, 27, 11, 11, 11, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 18, 18, 18, 27, 27, 27, 27, 11, 11, 11, 11, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001149767300 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 Building ZINC001149767300 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149767300 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 844) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149767300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767300 none COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 16, 17, 8, 16, 16, 28, 28, 28, 28, 28, 28, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 17, 17, 17, 28, 28, 28, 28, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 845) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001149767300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149767300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001149767300 none COC(=O)[C@@H](c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 11, 18, 18, 27, 27, 27, 27, 27, 27, 11, 11, 11, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 18, 18, 18, 27, 27, 27, 27, 11, 11, 11, 11, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001149767300 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001149767300 Building ZINC001150208217 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150208217 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/846 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001150208217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150208217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001150208217 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 34, 34, 34, 34, 34, 1, 1, 1, 10, 10, 10, 10, 10, 5, 16, 16, 16, 10, 10] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/847 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001150208217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150208217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001150208217 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 1, 1, 1, 11, 11, 11, 11, 11, 6, 16, 16, 16, 11, 11] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001150208217 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 Building ZINC001150208217 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150208217 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 846) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001150208217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150208217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001150208217 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 34, 34, 34, 34, 34, 1, 1, 1, 10, 10, 10, 10, 10, 5, 16, 16, 16, 10, 10] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 847) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001150208217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150208217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001150208217 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 1, 1, 1, 11, 11, 11, 11, 11, 6, 16, 16, 16, 11, 11] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001150208217 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001150208217 Building ZINC001151845048 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151845048 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/848 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001151845048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151845048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001151845048 none CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 34, 34, 27, 27, 27, 20, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 20, 20, 15, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/849 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001151845048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151845048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001151845048 none CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 33, 39, 39, 33, 33, 33, 21, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 33, 39, 39, 39, 39, 39, 39, 39, 39, 39, 33, 21, 21, 15, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001151845048 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 Building ZINC001151845048 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151845048 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 848) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001151845048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151845048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001151845048 none CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 34, 34, 27, 27, 27, 20, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 20, 20, 15, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 849) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001151845048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151845048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001151845048 none CC(C)(C)c1csc(CC2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 33, 39, 39, 33, 33, 33, 21, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 33, 39, 39, 39, 39, 39, 39, 39, 39, 39, 33, 21, 21, 15, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001151845048 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001151845048 Building ZINC001152229008 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152229008 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/850 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152229008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152229008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001152229008 none COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 5, 5, 3, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 3, 3, 3, 3, 11, 18, 18, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 3, 3, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [9, 10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/851 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152229008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152229008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001152229008 none COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 8, 13, 13, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 6, 6, 6, 6, 16, 26, 26, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152229008 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 Building ZINC001152229008 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152229008 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 850) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152229008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152229008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001152229008 none COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 5, 5, 3, 3, 3, 3, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 3, 3, 3, 3, 11, 18, 18, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 3, 3, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [9, 10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 851) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152229008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152229008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001152229008 none COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 8, 13, 13, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 6, 6, 6, 6, 16, 26, 26, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152229008 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152229008 Building ZINC001152238429 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152238429 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/852 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152238429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152238429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001152238429 none COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 7, 14, 14, 7, 7, 7, 7, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 7, 14, 24, 24, 31, 31, 31, 31, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/853 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152238429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152238429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001152238429 none COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 7, 11, 11, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 5, 5, 5, 5, 12, 22, 22, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11] 50 rigid atoms, others: [9, 10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152238429 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 Building ZINC001152238429 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152238429 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 852) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152238429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152238429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001152238429 none COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 7, 14, 14, 7, 7, 7, 7, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 7, 14, 24, 24, 31, 31, 31, 31, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 853) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1) `ZINC001152238429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152238429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001152238429 none COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)C[C@H]2NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 7, 11, 11, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 5, 5, 5, 5, 12, 22, 22, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11] 50 rigid atoms, others: [9, 10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152238429 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152238429 Building ZINC001152671235 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152671235 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/854 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C) `ZINC001152671235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152671235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001152671235 none CCOC(=O)c1sc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 23, 27, 23, 23, 7, 7, 7, 7, 3, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 23, 23, 23, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 23, 23, 23] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/855 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C) `ZINC001152671235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152671235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001152671235 none CCOC(=O)c1sc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 37, 28, 28, 8, 8, 8, 8, 4, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 28, 28, 28, 37, 37, 37, 37, 37, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 28, 28, 28] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152671235 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 Building ZINC001152671235 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152671235 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 854) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1sc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C) `ZINC001152671235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152671235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001152671235 none CCOC(=O)c1sc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 23, 27, 23, 23, 7, 7, 7, 7, 3, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 23, 23, 23, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 23, 23, 23] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 855) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1sc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C) `ZINC001152671235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152671235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001152671235 none CCOC(=O)c1sc(C2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 37, 28, 28, 8, 8, 8, 8, 4, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 28, 28, 28, 37, 37, 37, 37, 37, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 28, 28, 28] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152671235 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152671235 Building ZINC001152739089 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152739089 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/856 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1) `ZINC001152739089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152739089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001152739089 none COC(=O)c1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 36, 27, 27, 17, 17, 17, 17, 17, 17, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 36, 36, 36, 27, 17, 17, 17, 17, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/857 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1) `ZINC001152739089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152739089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001152739089 none COC(=O)c1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 36, 27, 27, 18, 18, 18, 18, 18, 18, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 36, 36, 36, 27, 18, 18, 18, 18, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152739089 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 Building ZINC001152739089 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152739089 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 856) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1) `ZINC001152739089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152739089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001152739089 none COC(=O)c1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 36, 27, 27, 17, 17, 17, 17, 17, 17, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 36, 36, 36, 27, 17, 17, 17, 17, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 857) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1) `ZINC001152739089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152739089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001152739089 none COC(=O)c1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 36, 27, 27, 18, 18, 18, 18, 18, 18, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 36, 36, 36, 27, 18, 18, 18, 18, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001152739089 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001152739089 Building ZINC001153950848 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153950848 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/858 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1) `ZINC001153950848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153950848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001153950848 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 23, 23, 23, 23, 23, 26, 23, 13, 13, 13, 13, 13, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 26, 23, 30, 30, 30, 23, 26, 26, 26, 23, 23, 13, 13, 7, 4, 4, 4, 4, 26, 26, 26, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/859 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1) `ZINC001153950848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153950848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001153950848 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 24, 24, 24, 24, 24, 25, 22, 13, 13, 13, 13, 13, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 27, 24, 29, 29, 29, 24, 25, 25, 25, 22, 22, 13, 13, 7, 4, 4, 4, 4, 27, 27, 27, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001153950848 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 Building ZINC001153950848 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153950848 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 858) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1) `ZINC001153950848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153950848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001153950848 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 23, 23, 23, 23, 23, 26, 23, 13, 13, 13, 13, 13, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 26, 23, 30, 30, 30, 23, 26, 26, 26, 23, 23, 13, 13, 7, 4, 4, 4, 4, 26, 26, 26, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 859) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1) `ZINC001153950848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153950848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001153950848 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 24, 24, 24, 24, 24, 25, 22, 13, 13, 13, 13, 13, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 27, 24, 29, 29, 29, 24, 25, 25, 25, 22, 22, 13, 13, 7, 4, 4, 4, 4, 27, 27, 27, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001153950848 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001153950848 Building ZINC001154742094 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154742094 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/860 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001154742094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154742094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001154742094 none O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 3, 16, 16, 23, 23, 23, 34, 48, 48, 34, 48, 48, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 3, 34, 48, 34, 48, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/861 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001154742094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154742094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001154742094 none O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 3, 16, 16, 23, 23, 23, 34, 48, 48, 34, 48, 48, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 9, 34, 48, 34, 48, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001154742094 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 Building ZINC001154742094 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154742094 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 860) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001154742094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154742094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001154742094 none O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 3, 16, 16, 23, 23, 23, 34, 48, 48, 34, 48, 48, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 3, 34, 48, 34, 48, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 861) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001154742094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154742094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001154742094 none O=C(Nc1cccc(S(=O)(=O)Nc2ncccn2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 3, 16, 16, 23, 23, 23, 34, 48, 48, 34, 48, 48, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 9, 34, 48, 34, 48, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001154742094 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001154742094 Building ZINC001155925333 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155925333 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/862 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2scnc2Br)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001155925333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155925333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155925333 none O=C(N1CCC(O)(c2scnc2Br)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 14, 1, 8, 1, 17, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 24, 17, 8, 8, 8, 8, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/863 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2scnc2Br)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001155925333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155925333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155925333 none O=C(N1CCC(O)(c2scnc2Br)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 14, 1, 8, 1, 17, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 6, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 24, 17, 8, 8, 8, 8, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001155925333 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 Building ZINC001155925333 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155925333 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 862) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2scnc2Br)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001155925333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155925333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155925333 none O=C(N1CCC(O)(c2scnc2Br)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 14, 1, 8, 1, 17, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 24, 17, 8, 8, 8, 8, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 863) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2scnc2Br)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001155925333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155925333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155925333 none O=C(N1CCC(O)(c2scnc2Br)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 14, 1, 8, 1, 17, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 6, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 24, 17, 8, 8, 8, 8, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001155925333 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001155925333 Building ZINC001156272537 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156272537 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/864 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1noc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001156272537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156272537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001156272537 none O=C(NCc1noc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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: [11, 1, 8, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 26, 26, 26, 26, 45, 45, 45, 45, 45, 45, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/865 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1noc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001156272537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156272537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001156272537 none O=C(NCc1noc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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: [11, 1, 8, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 26, 26, 26, 26, 45, 45, 45, 45, 45, 45, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156272537 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 Building ZINC001156272537 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156272537 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 864) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1noc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001156272537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156272537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001156272537 none O=C(NCc1noc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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: [11, 1, 8, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 26, 26, 26, 26, 45, 45, 45, 45, 45, 45, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 865) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1noc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001156272537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156272537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001156272537 none O=C(NCc1noc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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: [11, 1, 8, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 26, 26, 26, 26, 45, 45, 45, 45, 45, 45, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156272537 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156272537 Building ZINC001156511228 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511228 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/866 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511228 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 8, 14, 14, 14, 14, 32, 32, 44, 44, 44, 44, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/867 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511228 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 17, 17, 17, 17, 32, 32, 46, 46, 46, 46, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 17, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 17, 17, 17, 17] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 134 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511228 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 Building ZINC001156511228 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511228 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 866) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511228 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 8, 14, 14, 14, 14, 32, 32, 44, 44, 44, 44, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 867) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511228 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 17, 17, 17, 17, 32, 32, 46, 46, 46, 46, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 17, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 17, 17, 17, 17] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 134 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511228 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511228 Building ZINC001156511229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/868 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511229 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 15, 19, 19, 19, 19, 28, 28, 41, 41, 41, 41, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 15, 15, 19, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 19, 19, 19, 19] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 126 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/869 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511229 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 12, 15, 15, 15, 15, 27, 27, 41, 41, 41, 41, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 12, 12, 15, 15, 41, 41, 41, 41, 41, 41, 41, 41, 41, 15, 15, 15, 15] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 120 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 Building ZINC001156511229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 868) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511229 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 15, 19, 19, 19, 19, 28, 28, 41, 41, 41, 41, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 15, 15, 19, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 19, 19, 19, 19] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 126 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 869) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511229 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 12, 15, 15, 15, 15, 27, 27, 41, 41, 41, 41, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 12, 12, 15, 15, 41, 41, 41, 41, 41, 41, 41, 41, 41, 15, 15, 15, 15] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 120 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511229 Building ZINC001156511230 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511230 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/870 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511230 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 13, 16, 16, 16, 16, 28, 28, 42, 42, 42, 42, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 16, 16] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/871 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511230 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 16, 19, 19, 19, 19, 28, 28, 43, 43, 43, 43, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 16, 16, 19, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 19, 19, 19, 19] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511230 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 Building ZINC001156511230 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511230 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 870) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511230 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 13, 16, 16, 16, 16, 28, 28, 42, 42, 42, 42, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 16, 16] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 871) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511230 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 16, 19, 19, 19, 19, 28, 28, 43, 43, 43, 43, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 16, 16, 19, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 19, 19, 19, 19] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511230 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511230 Building ZINC001156511231 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511231 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/872 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511231 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 16, 16, 16, 31, 31, 46, 46, 46, 46, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 131 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/873 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511231 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 8, 14, 14, 14, 14, 32, 32, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 14, 14, 14, 14] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511231 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 Building ZINC001156511231 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156511231 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 872) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156511231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511231 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 16, 16, 16, 31, 31, 46, 46, 46, 46, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 131 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 873) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001156511231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156511231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001156511231 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 8, 14, 14, 14, 14, 32, 32, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 14, 14, 14, 14] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156511231 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156511231 Building ZINC001156831134 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156831134 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/874 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156831134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156831134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001156831134 none O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 23, 26, 26, 26, 33, 33, 33, 33, 33, 33, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 23, 33, 33, 33, 33, 33, 33, 33, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/875 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156831134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156831134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001156831134 none O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 22, 25, 25, 25, 32, 32, 32, 32, 32, 32, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 22, 32, 32, 32, 32, 32, 32, 32, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156831134 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 Building ZINC001156831134 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156831134 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 874) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156831134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156831134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001156831134 none O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 23, 26, 26, 26, 33, 33, 33, 33, 33, 33, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 23, 33, 33, 33, 33, 33, 33, 33, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 875) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156831134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156831134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001156831134 none O=C(Nc1ccc(NS(=O)(=O)Cc2ccccc2)cn1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 22, 25, 25, 25, 32, 32, 32, 32, 32, 32, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 22, 32, 32, 32, 32, 32, 32, 32, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001156831134 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001156831134 Building ZINC001157325937 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157325937 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/876 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001157325937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157325937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001157325937 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 3, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 46, 46, 46, 46, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/877 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001157325937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157325937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001157325937 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 3, 9, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 32, 32, 32, 32, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12] 32 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157325937 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 Building ZINC001157325937 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157325937 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 876) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001157325937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157325937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001157325937 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 3, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 46, 46, 46, 46, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 877) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001157325937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157325937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001157325937 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2OC2(CCN(C(=O)OC(C)(C)C)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 3, 9, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 32, 32, 32, 32, 12, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12] 32 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157325937 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157325937 Building ZINC001157388295 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001157388295 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/878 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/879 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/880 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/880' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/881 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/881' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157388295 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 Building ZINC001157388295 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001157388295 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 878) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 879) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 880) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 881) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157388295 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 Building ZINC001157388295 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001157388295 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 878) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 879) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 880) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 881) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157388295 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 Building ZINC001157388295 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001157388295 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 878) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 879) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 13, 17, 17, 17, 17, 17, 29, 31, 31, 30, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 29, 29, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `2' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 2 (index: 880) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `3' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 3 (index: 881) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001157388295.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001157388295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001157388295 none O=C(N1CCCN(Cc2ccccc2)CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 14, 16, 16, 16, 16, 16, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 28, 28, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157388295 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/1.* 3: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/3.* 2: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295/2.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157388295 Building ZINC001157624753 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157624753 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/882 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001157624753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157624753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157624753 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 19, 22, 29, 29, 29, 29, 29, 34, 34, 34, 34, 34, 29, 29, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 12, 12, 29, 29, 29, 29, 34, 34, 34, 34, 34, 29, 29, 29, 29, 3, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/883 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001157624753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157624753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157624753 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 19, 22, 29, 29, 29, 29, 29, 33, 33, 33, 33, 33, 29, 29, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 29, 29, 29, 29, 33, 33, 33, 33, 33, 29, 29, 29, 29, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157624753 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 Building ZINC001157624753 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157624753 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 882) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001157624753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157624753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157624753 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 19, 22, 29, 29, 29, 29, 29, 34, 34, 34, 34, 34, 29, 29, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 12, 12, 29, 29, 29, 29, 34, 34, 34, 34, 34, 29, 29, 29, 29, 3, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 883) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001157624753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157624753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157624753 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 19, 22, 29, 29, 29, 29, 29, 33, 33, 33, 33, 33, 29, 29, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 29, 29, 29, 29, 33, 33, 33, 33, 33, 29, 29, 29, 29, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157624753 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157624753 Building ZINC001157913478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157913478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/884 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl) `ZINC001157913478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157913478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157913478 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 26, 26, 26, 26, 6, 6, 6, 3, 3, 3, 5, 5, 5, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/885 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl) `ZINC001157913478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157913478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157913478 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 4, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 27, 27, 27, 27, 7, 7, 7, 4, 4, 4, 6, 6, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157913478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 Building ZINC001157913478 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157913478 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 884) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl) `ZINC001157913478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157913478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157913478 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 26, 26, 26, 26, 6, 6, 6, 3, 3, 3, 5, 5, 5, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 885) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl) `ZINC001157913478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157913478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001157913478 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 4, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 27, 27, 27, 27, 7, 7, 7, 4, 4, 4, 6, 6, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001157913478 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001157913478 Building ZINC001160593511 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160593511 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/886 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001160593511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160593511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001160593511 none O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 30, 48, 48, 48, 48, 48, 48, 48, 48, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 30, 48, 48, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/887 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001160593511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160593511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001160593511 none O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 30, 48, 48, 48, 48, 48, 48, 48, 48, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 30, 48, 48, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001160593511 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 Building ZINC001160593511 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160593511 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 886) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001160593511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160593511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001160593511 none O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 30, 48, 48, 48, 48, 48, 48, 48, 48, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 30, 48, 48, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 887) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001160593511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160593511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001160593511 none O=C(Nc1nnc(NS(=O)(=O)c2ccccc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 30, 48, 48, 48, 48, 48, 48, 48, 48, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 30, 48, 48, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001160593511 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160593511 Building ZINC001160841459 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160841459 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/888 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160841459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841459 none CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 41, 50, 23, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 23, 23, 8, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 50 rigid atoms, others: [50, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/889 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160841459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841459 none CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 10, 6, 6, 6, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 10, 10, 6, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001160841459 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 Building ZINC001160841459 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160841459 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 888) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160841459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841459 none CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 41, 50, 23, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 23, 23, 8, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 50 rigid atoms, others: [50, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 889) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160841459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841459 none CC(C)(C)OC(=O)NCc1cn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 10, 6, 6, 6, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 10, 10, 6, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001160841459 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841459 Building ZINC001160841460 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160841460 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/890 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160841460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841460 none CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 46, 21, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 35, 21, 21, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/891 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160841460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841460 none CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 38, 46, 18, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 38, 18, 18, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001160841460 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 Building ZINC001160841460 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160841460 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 890) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160841460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841460 none CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 46, 21, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 35, 21, 21, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 891) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1) `ZINC001160841460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160841460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001160841460 none CC(C)(C)OC(=O)NCc1cn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 38, 46, 18, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 38, 18, 18, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001160841460 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001160841460 Building ZINC001161103889 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161103889 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/892 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC001161103889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161103889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161103889 none O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 19, 19, 33, 33, 33, 19, 33, 33, 33, 11, 11, 11, 5, 2, 7, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 11, 11, 19, 33, 33, 33, 66, 11, 11, 11, 11, 11, 5, 6, 6, 5, 6, 6, 5, 11, 11, 11, 11] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/893 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC001161103889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161103889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161103889 none O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 9, 17, 17, 31, 31, 31, 17, 31, 31, 31, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 9, 9, 17, 31, 31, 31, 62, 9, 9, 9, 9, 9, 4, 5, 5, 4, 5, 5, 4, 9, 9, 9, 9] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161103889 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 Building ZINC001161103889 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161103889 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 892) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC001161103889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161103889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161103889 none O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 19, 19, 33, 33, 33, 19, 33, 33, 33, 11, 11, 11, 5, 2, 7, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 11, 11, 19, 33, 33, 33, 66, 11, 11, 11, 11, 11, 5, 6, 6, 5, 6, 6, 5, 11, 11, 11, 11] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 893) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC001161103889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161103889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161103889 none O=C(Nc1cc(Cl)ccc1O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 9, 17, 17, 31, 31, 31, 17, 31, 31, 31, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 9, 9, 17, 31, 31, 31, 62, 9, 9, 9, 9, 9, 4, 5, 5, 4, 5, 5, 4, 9, 9, 9, 9] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161103889 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161103889 Building ZINC001161133037 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161133037 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/894 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161133037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133037 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 10, 9, 12, 10, 15, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 11, 12, 36, 15, 15, 26, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/895 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161133037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133037 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 11, 10, 14, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 7, 7, 7, 4, 4, 2, 5, 5, 11, 11, 33, 14, 14, 27, 27, 27, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161133037 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 Building ZINC001161133037 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161133037 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 894) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161133037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133037 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 10, 9, 12, 10, 15, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 11, 12, 36, 15, 15, 26, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 895) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161133037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133037 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 11, 10, 14, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 7, 7, 7, 4, 4, 2, 5, 5, 11, 11, 33, 14, 14, 27, 27, 27, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161133037 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133037 Building ZINC001161133038 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161133038 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/896 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161133038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133038 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 11, 15, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 11, 11, 33, 15, 15, 29, 29, 29, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/897 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161133038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133038 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 10, 9, 12, 10, 15, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 11, 12, 36, 15, 15, 26, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161133038 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 Building ZINC001161133038 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161133038 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 896) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161133038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133038 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 11, 15, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 11, 11, 33, 15, 15, 29, 29, 29, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 897) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl) `ZINC001161133038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161133038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161133038 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2cc(F)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 10, 9, 12, 10, 15, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 11, 12, 36, 15, 15, 26, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161133038 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161133038 Building ZINC001161324597 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161324597 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/898 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1) `ZINC001161324597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161324597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324597 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/899 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1) `ZINC001161324597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161324597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324597 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 13, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 35 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161324597 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 Building ZINC001161324597 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161324597 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 898) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1) `ZINC001161324597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161324597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324597 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 899) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1) `ZINC001161324597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161324597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324597 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 13, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 35 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161324597 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324597 Building ZINC001161324608 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161324608 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/900 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1) `ZINC001161324608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161324608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324608 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/901 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1) `ZINC001161324608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161324608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324608 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 21, 21, 4, 21, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161324608 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 Building ZINC001161324608 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161324608 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 900) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1) `ZINC001161324608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161324608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324608 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 901) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1) `ZINC001161324608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161324608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001161324608 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[S@@](=O)C(C)(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 21, 21, 4, 21, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161324608 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161324608 Building ZINC001161401754 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161401754 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/902 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161401754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401754 none CCOC(=O)[C@@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 4, 17, 2, 4, 4, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/903 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161401754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401754 none CCOC(=O)[C@@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 25, 4, 25, 2, 4, 4, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161401754 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 Building ZINC001161401754 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161401754 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 902) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)[C@@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161401754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401754 none CCOC(=O)[C@@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 4, 17, 2, 4, 4, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 903) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)[C@@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161401754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401754 none CCOC(=O)[C@@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 25, 4, 25, 2, 4, 4, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161401754 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401754 Building ZINC001161401755 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161401755 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/904 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161401755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401755 none CCOC(=O)[C@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 22, 3, 6, 6, 3, 3, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 3, 22, 22, 22, 22, 22, 3, 3, 3, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 43, 49, 41, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 50, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 51, 52]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/905 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161401755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401755 none CCOC(=O)[C@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 4, 20, 2, 4, 4, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 2, 21, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161401755 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 Building ZINC001161401755 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161401755 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 904) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)[C@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161401755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401755 none CCOC(=O)[C@H](F)C1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 22, 3, 6, 6, 3, 3, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 3, 22, 22, 22, 22, 22, 3, 3, 3, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 43, 49, 41, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 50, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 51, 52]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 905) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)[C@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161401755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161401755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161401755 none CCOC(=O)[C@H](F)C1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', '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, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 4, 20, 2, 4, 4, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 2, 21, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161401755 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161401755 Building ZINC001161726675 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161726675 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/906 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O) `ZINC001161726675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161726675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726675 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 27, 27, 6, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 27, 27, 6, 27, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 69 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/907 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O) `ZINC001161726675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161726675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726675 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 30, 30, 8, 30, 30, 30, 30, 30, 30, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 30, 30, 8, 30, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161726675 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 Building ZINC001161726675 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161726675 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 906) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O) `ZINC001161726675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161726675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726675 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 27, 27, 6, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 27, 27, 6, 27, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 69 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 907) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O) `ZINC001161726675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161726675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726675 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 30, 30, 8, 30, 30, 30, 30, 30, 30, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 30, 30, 8, 30, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161726675 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726675 Building ZINC001161726676 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161726676 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/908 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O) `ZINC001161726676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161726676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726676 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 29, 29, 3, 29, 29, 29, 29, 29, 29, 3, 3, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 29, 29, 3, 29, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/909 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O) `ZINC001161726676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161726676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726676 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 27, 27, 3, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 27, 27, 3, 27, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161726676 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 Building ZINC001161726676 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161726676 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 908) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O) `ZINC001161726676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161726676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726676 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 29, 29, 3, 29, 29, 29, 29, 29, 29, 3, 3, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 29, 29, 3, 29, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 909) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O) `ZINC001161726676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161726676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001161726676 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CC[C@@H](C1)[S@]2=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 27, 27, 3, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 2, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 27, 27, 3, 27, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161726676 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161726676 Building ZINC001161727640 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161727640 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/910 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1) `ZINC001161727640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161727640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001161727640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 13, 4, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 11, 11, 9, 11, 11, 2, 2, 2, 2, 13, 13, 7, 13, 2, 2, 2, 2, 2, 6, 11, 11, 9, 11, 11, 2, 2] 150 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/911 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1) `ZINC001161727640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161727640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001161727640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 12, 12, 8, 12, 12, 3, 2, 2, 2, 18, 18, 6, 18, 2, 2, 2, 3, 3, 9, 12, 12, 8, 12, 12, 3, 3] 150 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161727640 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 Building ZINC001161727640 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161727640 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 910) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1) `ZINC001161727640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161727640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001161727640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 13, 4, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 11, 11, 9, 11, 11, 2, 2, 2, 2, 13, 13, 7, 13, 2, 2, 2, 2, 2, 6, 11, 11, 9, 11, 11, 2, 2] 150 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 911) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1) `ZINC001161727640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161727640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001161727640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](Oc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 12, 12, 8, 12, 12, 3, 2, 2, 2, 18, 18, 6, 18, 2, 2, 2, 3, 3, 9, 12, 12, 8, 12, 12, 3, 3] 150 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161727640 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161727640 Building ZINC001161837603 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161837603 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/912 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1) `ZINC001161837603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161837603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161837603 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 60 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/913 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1) `ZINC001161837603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161837603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161837603 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 13, 13, 13, 13, 13, 13, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161837603 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 Building ZINC001161837603 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161837603 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 912) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1) `ZINC001161837603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161837603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161837603 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 60 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 913) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1) `ZINC001161837603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161837603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161837603 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)C(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 13, 13, 13, 13, 13, 13, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001161837603 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001161837603 Building ZINC001220738496 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738496 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/914 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738496 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 11, 8, 15, 15, 15, 24, 24, 44, 44, 50, 50, 44, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 10, 11, 10, 11, 11, 15, 15, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 7, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 256 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/915 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738496 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 12, 10, 16, 16, 16, 26, 26, 44, 44, 49, 49, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 11, 11, 11, 12, 12, 12, 16, 16, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 256 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738496 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 Building ZINC001220738496 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738496 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 914) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738496 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 11, 8, 15, 15, 15, 24, 24, 44, 44, 50, 50, 44, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 10, 11, 10, 11, 11, 15, 15, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 7, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 256 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 915) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738496 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 12, 10, 16, 16, 16, 26, 26, 44, 44, 49, 49, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 11, 11, 11, 12, 12, 12, 16, 16, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 256 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738496 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738496 Building ZINC001220738497 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738497 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/916 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738497 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 8, 15, 15, 15, 23, 23, 43, 43, 49, 49, 43, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 10, 10, 9, 10, 10, 15, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 7, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 248 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/917 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738497 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 8, 13, 9, 16, 16, 16, 27, 27, 46, 46, 50, 50, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 12, 12, 12, 13, 13, 13, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 281 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738497 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 Building ZINC001220738497 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738497 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 916) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738497 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 8, 15, 15, 15, 23, 23, 43, 43, 49, 49, 43, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 10, 10, 9, 10, 10, 15, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 7, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 248 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 917) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738497 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 8, 13, 9, 16, 16, 16, 27, 27, 46, 46, 50, 50, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 12, 12, 12, 13, 13, 13, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 281 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738497 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738497 Building ZINC001220738498 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738498 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/918 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738498 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 12, 10, 16, 16, 16, 25, 25, 46, 46, 50, 50, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 12, 12, 12, 11, 12, 12, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 257 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/919 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738498 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 12, 13, 21, 18, 26, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 17, 17, 21, 17, 21, 21, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738498 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 Building ZINC001220738498 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738498 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 918) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738498 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 12, 10, 16, 16, 16, 25, 25, 46, 46, 50, 50, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 12, 12, 12, 11, 12, 12, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 257 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 919) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738498 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 12, 13, 21, 18, 26, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 17, 17, 21, 17, 21, 21, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738498 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738498 Building ZINC001220738499 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738499 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/920 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738499 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 14, 18, 16, 26, 26, 26, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 16, 16, 18, 16, 18, 18, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 215 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/921 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738499 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 13, 10, 18, 18, 18, 28, 28, 49, 49, 50, 50, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 12, 12, 13, 12, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 257 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738499 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 Building ZINC001220738499 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220738499 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 920) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220738499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738499 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 14, 18, 16, 26, 26, 26, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 16, 16, 18, 16, 18, 18, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 215 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 921) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220738499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220738499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220738499 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 13, 10, 18, 18, 18, 28, 28, 49, 49, 50, 50, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 12, 12, 13, 12, 13, 13, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 257 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220738499 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220738499 Building ZINC001220739006 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739006 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/922 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739006 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 17, 14, 11, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 35, 35, 47, 47, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 15, 15, 14, 13, 12, 12, 10, 10, 3, 2, 2, 1, 2, 2, 47, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 228 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/923 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739006 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 19, 16, 11, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 19, 21, 21, 31, 31, 40, 43, 31, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 19, 19, 17, 17, 15, 14, 15, 15, 13, 13, 4, 3, 3, 1, 3, 3, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 253 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739006 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 Building ZINC001220739006 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739006 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 922) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739006 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 17, 14, 11, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 35, 35, 47, 47, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 15, 15, 14, 13, 12, 12, 10, 10, 3, 2, 2, 1, 2, 2, 47, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 228 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 923) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739006 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 19, 16, 11, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 19, 21, 21, 31, 31, 40, 43, 31, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 19, 19, 17, 17, 15, 14, 15, 15, 13, 13, 4, 3, 3, 1, 3, 3, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 253 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739006 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739006 Building ZINC001220739007 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739007 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/924 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739007 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 11, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 14, 15, 15, 42, 42, 45, 46, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 11, 11, 11, 9, 9, 9, 7, 7, 3, 2, 2, 1, 2, 2, 46, 50, 50, 50, 50, 50, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 255 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/925 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739007 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 12, 9, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 14, 14, 14, 34, 34, 42, 47, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 12, 12, 10, 12, 11, 11, 11, 11, 3, 2, 2, 1, 2, 2, 47, 50, 50, 50, 50, 50, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 262 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739007 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 Building ZINC001220739007 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739007 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 924) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739007 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 11, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 14, 15, 15, 42, 42, 45, 46, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 11, 11, 11, 9, 9, 9, 7, 7, 3, 2, 2, 1, 2, 2, 46, 50, 50, 50, 50, 50, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 255 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 925) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001220739007 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 12, 9, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 14, 14, 14, 34, 34, 42, 47, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 12, 12, 10, 12, 11, 11, 11, 11, 3, 2, 2, 1, 2, 2, 47, 50, 50, 50, 50, 50, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 262 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739007 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739007 Building ZINC001220739130 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739130 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/926 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739130 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 14, 11, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 15, 30, 30, 46, 46, 49, 49, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 11, 11, 11, 11, 11, 11, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 49, 50, 50, 50, 50, 50, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 255 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/927 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739130 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 46, 46, 50, 50, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 7, 7, 7, 7, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [18, 17, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739130 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 Building ZINC001220739130 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739130 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 926) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739130 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 14, 11, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 15, 30, 30, 46, 46, 49, 49, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 11, 11, 11, 11, 11, 11, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 49, 50, 50, 50, 50, 50, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 255 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 927) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739130 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 46, 46, 50, 50, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 7, 7, 7, 7, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [18, 17, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739130 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739130 Building ZINC001220739131 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739131 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/928 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739131 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 10, 7, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 26, 26, 44, 44, 46, 46, 44, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 10, 10, 10, 10, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [18, 8, 10, 11, 12, 13, 14, 15, 16, 17, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 248 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/929 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739131 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 15, 10, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 28, 28, 46, 46, 48, 48, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 10, 10, 10, 10, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 48, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [18, 8, 10, 11, 12, 13, 14, 15, 16, 17, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739131 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 Building ZINC001220739131 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739131 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 928) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739131 none N[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 10, 7, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 26, 26, 44, 44, 46, 46, 44, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 10, 10, 10, 10, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [18, 8, 10, 11, 12, 13, 14, 15, 16, 17, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 248 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 929) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001220739131 none N[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 15, 10, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 28, 28, 46, 46, 48, 48, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 10, 10, 10, 10, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 48, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [18, 8, 10, 11, 12, 13, 14, 15, 16, 17, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739131 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739131 Building ZINC001220739364 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739364 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/930 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739364 none CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 15, 12, 22, 22, 22, 43, 43, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 15, 15, 15, 22, 22, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/931 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739364 none CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 16, 13, 24, 24, 24, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 16, 12, 16, 16, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 236 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739364 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 Building ZINC001220739364 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739364 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 930) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739364 none CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 15, 12, 22, 22, 22, 43, 43, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 15, 15, 15, 22, 22, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 931) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739364 none CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 16, 13, 24, 24, 24, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 16, 12, 16, 16, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 236 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739364 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739364 Building ZINC001220739365 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739365 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/932 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739365 none CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 12, 9, 19, 19, 19, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 12, 12, 12, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 236 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/933 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739365 none CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 14, 10, 20, 20, 20, 33, 33, 45, 45, 50, 50, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 14, 14, 14, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 259 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739365 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 Building ZINC001220739365 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001220739365 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 932) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001220739365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739365 none CC(C)C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 12, 9, 19, 19, 19, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 12, 12, 12, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 236 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 933) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21) `ZINC001220739365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001220739365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001220739365 none CC(C)C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)[C@@H](OC=O)C1c2ccccc2-c2ccccc21 NO_LONG_NAME dock 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', 'H', 'N.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 10, 1, 11, 5, 7, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 14, 10, 20, 20, 20, 33, 33, 45, 45, 50, 50, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 14, 14, 14, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 259 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001220739365 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001220739365 Building ZINC001221140174 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221140174 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/934 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O) `ZINC001221140174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221140174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221140174 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 3, 9, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 8, 8, 8, 8, 14, 14, 14, 8, 4, 4, 3, 15, 15, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/935 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O) `ZINC001221140174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221140174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221140174 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [15, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 3, 8, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 8, 4, 4, 3, 14, 14, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001221140174 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 Building ZINC001221140174 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221140174 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 934) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O) `ZINC001221140174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221140174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221140174 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 3, 9, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 8, 8, 8, 8, 14, 14, 14, 8, 4, 4, 3, 15, 15, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 935) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O) `ZINC001221140174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221140174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221140174 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC2(Cc3cccc(C(F)(F)F)c3)CCNCC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [15, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 3, 8, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 8, 4, 4, 3, 14, 14, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001221140174 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221140174 Building ZINC001221226200 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221226200 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/936 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O) `ZINC001221226200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001221226200 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 20, 20, 26, 28, 28, 28, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 8, 8, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/937 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O) `ZINC001221226200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001221226200 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [9, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 12, 12, 15, 15, 15, 15, 4, 4, 4, 4, 9, 9, 9, 4, 2, 2, 1, 10, 10, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001221226200 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 Building ZINC001221226200 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221226200 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 936) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O) `ZINC001221226200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001221226200 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 20, 20, 26, 28, 28, 28, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 8, 8, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 937) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O) `ZINC001221226200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001221226200 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)OC(C)(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [9, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 12, 12, 15, 15, 15, 15, 4, 4, 4, 4, 9, 9, 9, 4, 2, 2, 1, 10, 10, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001221226200 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221226200 Building ZINC001221353729 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221353729 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/938 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12) `ZINC001221353729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221353729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221353729 none Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 25, 27, 16, 25, 25, 19, 16, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 27, 25, 25, 19, 19, 19, 19, 19, 19, 13, 13, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/939 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12) `ZINC001221353729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221353729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221353729 none Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 22, 26, 13, 22, 22, 16, 12, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 26, 22, 22, 16, 16, 16, 16, 15, 15, 10, 10, 2, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001221353729 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 Building ZINC001221353729 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221353729 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 938) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12) `ZINC001221353729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221353729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221353729 none Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 25, 27, 16, 25, 25, 19, 16, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 27, 25, 25, 19, 19, 19, 19, 19, 19, 13, 13, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 939) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12) `ZINC001221353729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221353729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001221353729 none Cc1cc(=O)oc2cc(NC(=O)[C@@H](N)CCCCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 22, 26, 13, 22, 22, 16, 12, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 26, 22, 22, 16, 16, 16, 16, 15, 15, 10, 10, 2, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001221353729 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001221353729 Building ZINC001294227052 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294227052 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/940 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)c2)cc1Cl) `ZINC001294227052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294227052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001294227052 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 11, 11, 11, 21, 27, 27, 27, 27, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 21, 27, 27, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/941 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)c2)cc1Cl) `ZINC001294227052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294227052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001294227052 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 11, 11, 11, 22, 27, 27, 27, 27, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 4, 22, 27, 27, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001294227052 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 Building ZINC001294227052 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294227052 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 940) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)c2)cc1Cl) `ZINC001294227052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294227052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001294227052 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 11, 11, 11, 21, 27, 27, 27, 27, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 21, 27, 27, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 941) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)c2)cc1Cl) `ZINC001294227052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294227052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001294227052 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3nccs3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 8, 1, 1, 14, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 11, 11, 11, 22, 27, 27, 27, 27, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 4, 22, 27, 27, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001294227052 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294227052 Building ZINC001294262647 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294262647 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/942 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1) `ZINC001294262647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294262647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001294262647 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 14, 15, 18, 18, 18, 18, 35, 35, 35, 35, 35, 35, 18, 18, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 6, 6, 18, 18, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 162 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/943 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1) `ZINC001294262647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294262647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001294262647 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 11, 15, 19, 19, 19, 19, 42, 42, 42, 42, 42, 42, 19, 19, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 7, 7, 19, 19, 19, 19, 19, 42, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001294262647 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 Building ZINC001294262647 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294262647 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 942) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1) `ZINC001294262647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294262647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001294262647 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 14, 15, 18, 18, 18, 18, 35, 35, 35, 35, 35, 35, 18, 18, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 6, 6, 18, 18, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 162 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 943) grep: /scratch/xiaobo/236261/xbz-8058088.52/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1) `ZINC001294262647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294262647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001294262647 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCC(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 11, 15, 19, 19, 19, 19, 42, 42, 42, 42, 42, 42, 19, 19, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 7, 7, 19, 19, 19, 19, 19, 42, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001294262647 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001294262647 Building ZINC001295406087 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001295406087 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/944 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001295406087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406087 none NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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: [47, 37, 47, 18, 37, 37, 40, 40, 37, 40, 40, 40, 18, 18, 18, 8, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 47, 47, 40, 40, 40, 40, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/945 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001295406087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406087 none NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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: [45, 33, 45, 17, 33, 33, 37, 37, 33, 37, 37, 37, 17, 17, 17, 6, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 45, 45, 37, 37, 37, 37, 17, 17, 17, 17, 3, 1, 3, 17, 17, 17, 17] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001295406087 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 Building ZINC001295406087 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001295406087 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 944) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001295406087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406087 none NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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: [47, 37, 47, 18, 37, 37, 40, 40, 37, 40, 40, 40, 18, 18, 18, 8, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 47, 47, 40, 40, 40, 40, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 945) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001295406087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406087 none NC(=O)[C@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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: [45, 33, 45, 17, 33, 33, 37, 37, 33, 37, 37, 37, 17, 17, 17, 6, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 45, 45, 37, 37, 37, 37, 17, 17, 17, 17, 3, 1, 3, 17, 17, 17, 17] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001295406087 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406087 Building ZINC001295406088 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001295406088 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/946 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001295406088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406088 none NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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: [41, 31, 41, 18, 31, 31, 35, 35, 31, 31, 35, 35, 18, 18, 18, 8, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 41, 41, 35, 35, 35, 35, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/947 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001295406088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406088 none NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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, 30, 48, 15, 30, 30, 34, 34, 30, 30, 34, 34, 15, 15, 15, 6, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 48, 48, 34, 34, 34, 34, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001295406088 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 Building ZINC001295406088 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001295406088 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 946) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001295406088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406088 none NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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: [41, 31, 41, 18, 31, 31, 35, 35, 31, 31, 35, 35, 18, 18, 18, 8, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 41, 41, 35, 35, 35, 35, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 947) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001295406088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001295406088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001295406088 none NC(=O)[C@@H](c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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, 30, 48, 15, 30, 30, 34, 34, 30, 30, 34, 34, 15, 15, 15, 6, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 48, 48, 34, 34, 34, 34, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001295406088 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001295406088 Building ZINC001297427214 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001297427214 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/948 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1) `ZINC001297427214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001297427214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001297427214 none CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', '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, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 31, 31, 31, 31, 31, 31, 13, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/949 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1) `ZINC001297427214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001297427214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001297427214 none CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', '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, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 31, 31, 31, 31, 31, 31, 14, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001297427214 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 Building ZINC001297427214 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001297427214 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 948) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1) `ZINC001297427214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001297427214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001297427214 none CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', '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, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 31, 31, 31, 31, 31, 31, 13, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 949) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1) `ZINC001297427214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001297427214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001297427214 none CCc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', '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, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 31, 31, 31, 31, 31, 31, 14, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001297427214 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297427214 Building ZINC001297685599 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001297685599 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/950 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C) `ZINC001297685599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001297685599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001297685599 none CCOC(=O)c1cnn(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 39, 15, 39, 15, 15, 15, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 15, 15, 40, 40, 40, 40, 40, 15, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 15, 15, 15] 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]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/951 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C) `ZINC001297685599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001297685599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001297685599 none CCOC(=O)c1cnn(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 34, 16, 16, 16, 6, 6, 6, 6, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 16, 16, 34, 34, 34, 34, 34, 16, 6, 6, 6, 6, 6, 3, 3, 6, 6, 6, 6, 16, 16, 16] 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]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001297685599 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 Building ZINC001297685599 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001297685599 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 950) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1cnn(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C) `ZINC001297685599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001297685599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001297685599 none CCOC(=O)c1cnn(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 39, 15, 39, 15, 15, 15, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 15, 15, 40, 40, 40, 40, 40, 15, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 15, 15, 15] 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]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 951) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CCOC(=O)c1cnn(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C) `ZINC001297685599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001297685599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001297685599 none CCOC(=O)c1cnn(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 34, 16, 16, 16, 6, 6, 6, 6, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 16, 16, 34, 34, 34, 34, 34, 16, 6, 6, 6, 6, 6, 3, 3, 6, 6, 6, 6, 16, 16, 16] 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]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001297685599 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001297685599 Building ZINC001298635094 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001298635094 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/952 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001298635094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001298635094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001298635094 none CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 22, 34, 22, 22, 22, 22, 22, 22, 22, 22, 5, 2, 13, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 2, 1, 2, 22, 22, 22, 22] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/953 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001298635094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001298635094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001298635094 none CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 22, 36, 22, 22, 22, 22, 22, 22, 22, 22, 5, 2, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 3, 1, 3, 22, 22, 22, 22] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001298635094 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 Building ZINC001298635094 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001298635094 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 952) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001298635094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001298635094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001298635094 none CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 22, 34, 22, 22, 22, 22, 22, 22, 22, 22, 5, 2, 13, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 2, 1, 2, 22, 22, 22, 22] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 953) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001298635094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001298635094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001298635094 none CC(C)(C)OC(=O)N1CCC2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 22, 36, 22, 22, 22, 22, 22, 22, 22, 22, 5, 2, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 3, 1, 3, 22, 22, 22, 22] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001298635094 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001298635094 Building ZINC001299078769 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001299078769 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/954 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001299078769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078769 none O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 17, 15, 17, 16, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 17, 16, 51, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 182 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/955 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001299078769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078769 none O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 17, 16, 18, 17, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 18, 17, 54, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001299078769 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 Building ZINC001299078769 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001299078769 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 954) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001299078769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078769 none O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 17, 15, 17, 16, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 17, 16, 51, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 182 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 955) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001299078769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078769 none O=C(NC[C@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 17, 16, 18, 17, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 18, 17, 54, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001299078769 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078769 Building ZINC001299078770 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001299078770 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/956 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001299078770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078770 none O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 17, 16, 18, 17, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 17, 18, 54, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/957 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001299078770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078770 none O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 17, 16, 17, 16, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 17, 17, 51, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001299078770 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 Building ZINC001299078770 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001299078770 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 956) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001299078770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078770 none O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 17, 16, 18, 17, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 17, 18, 54, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 957) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001299078770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001299078770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001299078770 none O=C(NC[C@@H](CO)Cc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 17, 16, 17, 16, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 17, 17, 51, 19, 19, 35, 35, 35, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001299078770 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299078770 Building ZINC001299919229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001299919229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/958 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001299919229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001299919229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001299919229 none CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 4, 5, 2, 4, 4, 6, 14, 14, 14, 22, 27, 27, 24, 27, 27, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 27, 27, 27, 27, 27, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/959 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001299919229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001299919229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001299919229 none CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 6, 7, 2, 6, 6, 7, 19, 19, 19, 25, 28, 28, 26, 28, 28, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 25, 25, 28, 28, 28, 28, 28, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001299919229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 Building ZINC001299919229 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001299919229 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 958) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001299919229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001299919229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001299919229 none CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 4, 5, 2, 4, 4, 6, 14, 14, 14, 22, 27, 27, 24, 27, 27, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 27, 27, 27, 27, 27, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 959) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001299919229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001299919229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001299919229 none CC(C)(C)OC(=O)[C@H](CC(=O)OCc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 6, 7, 2, 6, 6, 7, 19, 19, 19, 25, 28, 28, 26, 28, 28, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 25, 25, 28, 28, 28, 28, 28, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001299919229 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001299919229 Building ZINC001303260842 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260842 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/960 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260842 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 28, 28, 28, 28, 8, 8, 4, 4, 4, 6, 6, 6, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/961 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260842 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 5, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 27, 27, 27, 27, 11, 11, 2, 2, 2, 5, 5, 5, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260842 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 Building ZINC001303260842 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260842 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 960) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260842 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 28, 28, 28, 28, 8, 8, 4, 4, 4, 6, 6, 6, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 961) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260842 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 5, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 27, 27, 27, 27, 11, 11, 2, 2, 2, 5, 5, 5, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260842 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260842 Building ZINC001303260843 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260843 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/962 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260843 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 28, 28, 28, 28, 9, 9, 6, 6, 6, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/963 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260843 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 26, 26, 26, 26, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260843 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 Building ZINC001303260843 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260843 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 962) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260843 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 28, 28, 28, 28, 9, 9, 6, 6, 6, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 963) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260843 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 26, 26, 26, 26, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260843 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260843 Building ZINC001303260844 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260844 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/964 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260844 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 27, 27, 27, 27, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/965 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260844 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 28, 28, 28, 28, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260844 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 Building ZINC001303260844 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260844 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 964) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260844 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 27, 27, 27, 27, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 965) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260844 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)O[C@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 28, 28, 28, 28, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260844 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260844 Building ZINC001303260845 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260845 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/966 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260845 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 23, 23, 26, 26, 26, 26, 13, 13, 4, 4, 4, 6, 6, 6, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/967 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260845 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 28, 28, 28, 28, 13, 13, 3, 3, 3, 5, 5, 5, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 13, 13, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260845 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 Building ZINC001303260845 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303260845 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 966) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303260845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260845 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 23, 23, 26, 26, 26, 26, 13, 13, 4, 4, 4, 6, 6, 6, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 967) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001303260845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303260845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001303260845 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)O[C@@]3(CCN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 28, 28, 28, 28, 13, 13, 3, 3, 3, 5, 5, 5, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 13, 13, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303260845 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303260845 Building ZINC001303300798 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303300798 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/968 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001303300798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303300798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001303300798 none Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.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', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 36, 36, 13, 13, 13, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 36, 36, 36, 36, 36, 36, 36, 13, 13, 13, 13, 13, 6, 6, 13, 13, 13, 13, 36, 36] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/969 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001303300798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303300798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001303300798 none Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.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', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 15, 36, 36, 15, 15, 15, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 4, 4, 15, 15, 15, 15, 36, 36] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303300798 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 Building ZINC001303300798 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303300798 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 968) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001303300798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303300798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001303300798 none Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.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', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 36, 36, 13, 13, 13, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 36, 36, 36, 36, 36, 36, 36, 13, 13, 13, 13, 13, 6, 6, 13, 13, 13, 13, 36, 36] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 969) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001303300798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303300798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001303300798 none Cc1ccc(S(=O)(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.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', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 15, 36, 36, 15, 15, 15, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 4, 4, 15, 15, 15, 15, 36, 36] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303300798 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303300798 Building ZINC001303374824 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303374824 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/970 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1) `ZINC001303374824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303374824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303374824 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 16, 16, 30, 31, 31, 31, 10, 10, 10, 10, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/971 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1) `ZINC001303374824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303374824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303374824 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 8, 15, 15, 28, 28, 28, 28, 8, 8, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 84 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303374824 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 Building ZINC001303374824 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303374824 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 970) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1) `ZINC001303374824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303374824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303374824 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 16, 16, 30, 31, 31, 31, 10, 10, 10, 10, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 971) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1) `ZINC001303374824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303374824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303374824 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)OC(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 8, 15, 15, 28, 28, 28, 28, 8, 8, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 84 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303374824 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303374824 Building ZINC001303611232 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303611232 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/972 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303611232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611232 none CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 15, 20, 33, 33, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 33, 33, 33, 33, 33, 33, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/973 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303611232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611232 none CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 16, 22, 31, 31, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 16, 16, 31, 31, 31, 31, 31, 31, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303611232 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 Building ZINC001303611232 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303611232 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 972) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303611232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611232 none CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 15, 20, 33, 33, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 33, 33, 33, 33, 33, 33, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 973) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303611232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611232 none CN(Cc1nnc2n1C[C@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 16, 22, 31, 31, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 16, 16, 31, 31, 31, 31, 31, 31, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303611232 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611232 Building ZINC001303611233 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303611233 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/974 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303611233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611233 none CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 17, 22, 32, 32, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 17, 17, 32, 32, 32, 32, 32, 32, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/975 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303611233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611233 none CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 15, 20, 33, 33, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 33, 33, 33, 33, 33, 33, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303611233 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 Building ZINC001303611233 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303611233 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 974) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303611233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611233 none CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 17, 22, 32, 32, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 17, 17, 32, 32, 32, 32, 32, 32, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 975) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001303611233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303611233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001303611233 none CN(Cc1nnc2n1C[C@@H](C(F)(F)F)CC2)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 15, 20, 33, 33, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 33, 33, 33, 33, 33, 33, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303611233 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303611233 Building ZINC001303795528 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303795528 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/976 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1) `ZINC001303795528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303795528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001303795528 none Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 10, 11, 11, 6, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 32, 21, 11, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/977 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1) `ZINC001303795528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303795528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001303795528 none Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 3, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 33, 33, 33, 33, 21, 11, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303795528 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 Building ZINC001303795528 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303795528 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 976) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1) `ZINC001303795528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303795528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001303795528 none Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 10, 11, 11, 6, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 32, 21, 11, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 977) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1) `ZINC001303795528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303795528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001303795528 none Cc1nnc(NS(=O)(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 3, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 33, 33, 33, 33, 21, 11, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303795528 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303795528 Building ZINC001303806000 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303806000 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/978 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303806000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806000 none CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 39, 26, 39, 26, 26, 26, 26, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 26, 26, 26, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43, 26, 26, 26, 26, 26, 26, 14, 14, 3, 7, 7, 26, 26, 26, 26] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/979 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303806000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806000 none CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 35, 23, 35, 23, 23, 23, 23, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 23, 23, 23, 23, 23, 12, 12, 2, 7, 7, 23, 23, 23, 23] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303806000 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 Building ZINC001303806000 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303806000 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 978) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303806000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806000 none CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 39, 26, 39, 26, 26, 26, 26, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 25, 26, 26, 26, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43, 26, 26, 26, 26, 26, 26, 14, 14, 3, 7, 7, 26, 26, 26, 26] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 979) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303806000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806000 none CC(C)(C)OC(=O)N1CCC2(C[C@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 35, 23, 35, 23, 23, 23, 23, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 23, 23, 23, 23, 23, 12, 12, 2, 7, 7, 23, 23, 23, 23] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303806000 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806000 Building ZINC001303806001 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303806001 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/980 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303806001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806001 none CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 28, 40, 28, 28, 28, 28, 26, 16, 28, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 6, 28, 28, 28, 28] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/981 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303806001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806001 none CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 31, 42, 31, 31, 31, 31, 27, 14, 30, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 31, 31, 31, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 31, 12, 12, 3, 6, 6, 31, 31, 31, 31] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303806001 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 Building ZINC001303806001 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303806001 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 980) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303806001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806001 none CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 28, 40, 28, 28, 28, 28, 26, 16, 28, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 6, 28, 28, 28, 28] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 981) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1) `ZINC001303806001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303806001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001303806001 none CC(C)(C)OC(=O)N1CCC2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)OC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 31, 42, 31, 31, 31, 31, 27, 14, 30, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 31, 31, 31, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 31, 12, 12, 3, 6, 6, 31, 31, 31, 31] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303806001 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303806001 Building ZINC001303996180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303996180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/982 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2ncc(I)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001303996180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303996180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001303996180 none O=C(N1CCn2ncc(I)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 18, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [6, 1, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 5, 1, 5] 33 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/983 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2ncc(I)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001303996180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303996180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001303996180 none O=C(N1CCn2ncc(I)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 18, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [6, 1, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 5, 1, 5] 33 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303996180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 Building ZINC001303996180 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303996180 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 982) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2ncc(I)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001303996180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303996180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001303996180 none O=C(N1CCn2ncc(I)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 18, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [6, 1, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 5, 1, 5] 33 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 983) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(N1CCn2ncc(I)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001303996180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303996180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001303996180 none O=C(N1CCn2ncc(I)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 8, 1, 1, 18, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [6, 1, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 5, 1, 5] 33 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001303996180 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001303996180 Building ZINC001306263821 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306263821 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/984 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cn1) `ZINC001306263821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306263821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001306263821 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 8, 12, 12, 21, 21, 21, 33, 34, 34, 33, 33, 34, 34, 12, 4, 4, 4, 4, 4, 4, 2, 12, 12, 33, 34, 34, 34, 34, 12, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/985 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cn1) `ZINC001306263821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306263821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001306263821 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 8, 12, 12, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 12, 4, 4, 4, 4, 4, 4, 2, 12, 12, 33, 33, 33, 33, 33, 12, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306263821 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 Building ZINC001306263821 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306263821 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 984) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cn1) `ZINC001306263821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306263821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001306263821 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 8, 12, 12, 21, 21, 21, 33, 34, 34, 33, 33, 34, 34, 12, 4, 4, 4, 4, 4, 4, 2, 12, 12, 33, 34, 34, 34, 34, 12, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 985) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cn1) `ZINC001306263821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306263821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001306263821 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 8, 12, 12, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 12, 4, 4, 4, 4, 4, 4, 2, 12, 12, 33, 33, 33, 33, 33, 12, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306263821 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306263821 Building ZINC001306522356 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306522356 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/986 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001306522356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306522356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306522356 none O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 28, 28, 11, 28, 28, 28, 28, 11, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 28, 28, 28, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/987 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001306522356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306522356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306522356 none O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 28, 28, 11, 28, 28, 28, 28, 11, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 28, 28, 28, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306522356 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 Building ZINC001306522356 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306522356 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 986) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001306522356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306522356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306522356 none O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 28, 28, 11, 28, 28, 28, 28, 11, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 28, 28, 28, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 987) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001306522356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306522356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306522356 none O=C(Nc1n[nH]c(c2ccc(Br)cc2F)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 28, 28, 11, 28, 28, 28, 28, 11, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 28, 28, 28, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306522356 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306522356 Building ZINC001306817566 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306817566 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/988 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1) `ZINC001306817566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306817566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001306817566 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 8, 9, 11, 11, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 9, 9, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/989 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1) `ZINC001306817566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306817566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001306817566 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 6, 8, 15, 15, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 8, 8, 15, 15, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306817566 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 Building ZINC001306817566 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306817566 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 988) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1) `ZINC001306817566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306817566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001306817566 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 8, 9, 11, 11, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 9, 9, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 989) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1) `ZINC001306817566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306817566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001306817566 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 6, 8, 15, 15, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 8, 8, 15, 15, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306817566 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306817566 Building ZINC001306841374 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841374 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/990 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O) `ZINC001306841374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841374 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/991 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O) `ZINC001306841374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841374 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 5, 5, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841374 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 Building ZINC001306841374 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841374 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 990) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O) `ZINC001306841374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841374 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 991) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O) `ZINC001306841374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841374 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 5, 5, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841374 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841374 Building ZINC001306841375 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841375 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/992 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O) `ZINC001306841375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841375 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/993 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O) `ZINC001306841375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841375 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841375 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 Building ZINC001306841375 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841375 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 992) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O) `ZINC001306841375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841375 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 993) grep: /scratch/xiaobo/236261/xbz-8058088.52/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O) `ZINC001306841375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841375 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841375 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841375 Building ZINC001306841376 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841376 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/994 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O) `ZINC001306841376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841376 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 4, 14, 14, 14, 14, 14, 14, 2, 2, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 2, 2, 2, 14, 14, 4, 14, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/995 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O) `ZINC001306841376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841376 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 57 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841376 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 Building ZINC001306841376 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841376 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 994) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O) `ZINC001306841376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841376 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 4, 14, 14, 14, 14, 14, 14, 2, 2, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 2, 2, 2, 14, 14, 4, 14, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 995) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O) `ZINC001306841376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841376 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 57 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841376 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841376 Building ZINC001306841377 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841377 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/996 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O) `ZINC001306841377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841377 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 18, 18, 3, 18, 18, 18, 18, 18, 18, 2, 2, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 5, 5, 2, 2, 2, 18, 18, 4, 18, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/997 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O) `ZINC001306841377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841377 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 12, 12, 12, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841377 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 Building ZINC001306841377 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306841377 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 996) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O) `ZINC001306841377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306841377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841377 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 18, 18, 3, 18, 18, 18, 18, 18, 18, 2, 2, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 5, 5, 2, 2, 2, 18, 18, 4, 18, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 997) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O) `ZINC001306841377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306841377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306841377 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 12, 12, 12, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306841377 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306841377 Building ZINC001306868987 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306868987 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/998 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O) `ZINC001306868987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306868987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306868987 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 11, 11, 17, 17, 17, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/999 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O) `ZINC001306868987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306868987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306868987 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 11, 11, 16, 16, 16, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306868987 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 Building ZINC001306868987 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306868987 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 998) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O) `ZINC001306868987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306868987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306868987 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 11, 11, 17, 17, 17, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 mkdir: created directory `1' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/1 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 1 (index: 999) grep: /scratch/xiaobo/236261/xbz-8058088.52/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O) `ZINC001306868987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306868987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001306868987 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 11, 11, 16, 16, 16, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001306868987 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/0.* 1: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987/1.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001306868987 Building ZINC001317866772 mkdir: created directory `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001317866772 mkdir: created directory `0' /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772/0 /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/236261/xbz-8058088.52/working/3D/1000 `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1NS(C)(=O)=O) `ZINC001317866772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001317866772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001317866772 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1NS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 13, 13, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 13, 13, 13, 13, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772 /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Finished preparing ZINC001317866772 Recording results /scratch/xiaobo/236261/xbz-8058088.52/working /scratch/xiaobo/236261/xbz-8058088.52 Appending to /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.* 0: /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772/0.* Removing working files in /scratch/xiaobo/236261/xbz-8058088.52/working/building/ZINC001317866772 /scratch/xiaobo/236261/xbz-8058088.52 Compressing combined databse files /scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/236261/xbz-8058088.52/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/236261/xbz-8058088.52/working/3D/1001' removed directory: `/scratch/xiaobo/236261/xbz-8058088.52/working/3D' rmdir: removing directory, `/scratch/xiaobo/236261/xbz-8058088.52/working/building' rmdir: removing directory, `/scratch/xiaobo/236261/xbz-8058088.52/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/236261/xbz-8058088.52' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbz' `/scratch/xiaobo/236261/xbz-8058088.52/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbz/finished' `/scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbz/finished/xbz.db2.gz' removed `/scratch/xiaobo/236261/xbz-8058088.52/finished/xbz.db2.gz' removed directory: `/scratch/xiaobo/236261/xbz-8058088.52/finished' removed directory: `/scratch/xiaobo/236261/xbz-8058088.52'